{ "cells": [ { "cell_type": "markdown", "metadata": {}, "source": [ "# Characterizing the general methylation landscape" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "In this notebook, I will characterize the general methylation landscape. This will provide context I need to understand the significance of differentially methylated loci I obtain with `methylKit`. To characterize CpG methylation, I will use individual samples, as well as a union BEDgraph that concatenates all sample information.\n", "\n", "1. Concatenate coverage information\n", "2. Characterize methylation for each CpG dinucleotide in individual samples and union BEDgraph\n", "2. Determine genomic location of methylated, sparsely methylated, and unmethylated CpGs" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "## 0. Set working directory" ] }, { "cell_type": "code", "execution_count": 1, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "/Users/yaamini/Documents/project-oyster-oa/code/Haws\r\n" ] } ], "source": [ "!pwd" ] }, { "cell_type": "code", "execution_count": 2, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "/Users/yaamini/Documents/project-oyster-oa/analyses\n" ] } ], "source": [ "cd ../../analyses/" ] }, { "cell_type": "code", "execution_count": 3, "metadata": { "collapsed": true }, "outputs": [], "source": [ "#!mkdir Haws_06-methylation-landscape" ] }, { "cell_type": "code", "execution_count": 3, "metadata": { "collapsed": false, "scrolled": true }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "/Users/yaamini/Documents/project-oyster-oa/analyses/Haws_06-methylation-landscape\n" ] } ], "source": [ "cd Haws_06-methylation-landscape/" ] }, { "cell_type": "code", "execution_count": 4, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "0.18.1\n" ] } ], "source": [ "#Install pandas for this notebook\n", "import pandas as pd\n", "print(pd.__version__)" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "## 1. Obtain sample BEDgraphs" ] }, { "cell_type": "code", "execution_count": 6, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "--2021-05-17 20:50:07-- https://gannet.fish.washington.edu/spartina/project-oyster-oa/Haws/bismark-2/\n", "Resolving gannet.fish.washington.edu (gannet.fish.washington.edu)... 128.95.149.52\n", "Connecting to gannet.fish.washington.edu (gannet.fish.washington.edu)|128.95.149.52|:443... connected.\n", "WARNING: cannot verify gannet.fish.washington.edu's certificate, issued by ‘CN=InCommon RSA Server CA,OU=InCommon,O=Internet2,L=Ann Arbor,ST=MI,C=US’:\n", " Unable to locally verify the issuer's authority.\n", "HTTP request sent, awaiting response... 200 OK\n", "Length: unspecified [text/html]\n", "Saving to: ‘./index.html.tmp’\n", "\n", "index.html.tmp [ <=> ] 168.69K --.-KB/s in 0.004s \n", "\n", "2021-05-17 20:50:12 (45.3 MB/s) - ‘./index.html.tmp’ saved [172743]\n", "\n", "Loading robots.txt; please ignore errors.\n", "--2021-05-17 20:50:12-- https://gannet.fish.washington.edu/robots.txt\n", "Reusing existing connection to gannet.fish.washington.edu:443.\n", "HTTP request sent, awaiting response... 404 Not Found\n", "2021-05-17 20:50:12 ERROR 404: Not Found.\n", "\n", "Removing ./index.html.tmp since it should be rejected.\n", "\n", "--2021-05-17 20:50:12-- https://gannet.fish.washington.edu/spartina/project-oyster-oa/Haws/bismark-2/?C=N;O=D\n", "Reusing existing connection to gannet.fish.washington.edu:443.\n", "HTTP request sent, awaiting response... 200 OK\n", "Length: unspecified [text/html]\n", "Saving to: ‘./index.html?C=N;O=D.tmp’\n", "\n", "index.html?C=N;O=D. [ <=> ] 168.69K --.-KB/s in 0.003s \n", "\n", "2021-05-17 20:50:16 (59.2 MB/s) - ‘./index.html?C=N;O=D.tmp’ saved [172743]\n", "\n", "Removing ./index.html?C=N;O=D.tmp since it should be rejected.\n", "\n", "--2021-05-17 20:50:16-- https://gannet.fish.washington.edu/spartina/project-oyster-oa/Haws/bismark-2/?C=M;O=A\n", "Reusing existing connection to gannet.fish.washington.edu:443.\n", "HTTP request sent, awaiting response... 200 OK\n", "Length: unspecified [text/html]\n", "Saving to: ‘./index.html?C=M;O=A.tmp’\n", "\n", "index.html?C=M;O=A. [ <=> ] 168.69K --.-KB/s in 0.003s \n", "\n", "2021-05-17 20:50:21 (57.9 MB/s) - ‘./index.html?C=M;O=A.tmp’ saved [172743]\n", "\n", "Removing ./index.html?C=M;O=A.tmp since it should be rejected.\n", "\n", "--2021-05-17 20:50:21-- https://gannet.fish.washington.edu/spartina/project-oyster-oa/Haws/bismark-2/?C=S;O=A\n", "Reusing existing connection to gannet.fish.washington.edu:443.\n", "HTTP request sent, awaiting response... 200 OK\n", "Length: unspecified [text/html]\n", "Saving to: ‘./index.html?C=S;O=A.tmp’\n", "\n", "index.html?C=S;O=A. [ <=> ] 168.69K --.-KB/s in 0.003s \n", "\n", "2021-05-17 20:50:26 (54.9 MB/s) - ‘./index.html?C=S;O=A.tmp’ saved [172743]\n", "\n", "Removing ./index.html?C=S;O=A.tmp since it should be rejected.\n", "\n", "--2021-05-17 20:50:26-- https://gannet.fish.washington.edu/spartina/project-oyster-oa/Haws/bismark-2/?C=D;O=A\n", "Reusing existing connection to gannet.fish.washington.edu:443.\n", "HTTP request sent, awaiting response... 200 OK\n", "Length: unspecified [text/html]\n", "Saving to: ‘./index.html?C=D;O=A.tmp’\n", "\n", "index.html?C=D;O=A. [ <=> ] 168.69K --.-KB/s in 0.003s \n", "\n", "2021-05-17 20:50:30 (52.7 MB/s) - ‘./index.html?C=D;O=A.tmp’ saved [172743]\n", "\n", "Removing ./index.html?C=D;O=A.tmp since it should be rejected.\n", "\n", "--2021-05-17 20:50:30-- https://gannet.fish.washington.edu/spartina/project-oyster-oa/Haws/bismark-2/bismark_summary_report.html\n", "Reusing existing connection to gannet.fish.washington.edu:443.\n", "HTTP request sent, awaiting response... 200 OK\n", "Length: 3192063 (3.0M) [text/html]\n", "Saving to: ‘./bismark_summary_report.html.tmp’\n", "\n", "bismark_summary_rep 100%[===================>] 3.04M --.-KB/s in 0.06s \n", "\n", "2021-05-17 20:50:30 (49.8 MB/s) - ‘./bismark_summary_report.html.tmp’ saved [3192063/3192063]\n", "\n", "Removing ./bismark_summary_report.html.tmp since it should be rejected.\n", "\n", "--2021-05-17 20:50:31-- https://gannet.fish.washington.edu/spartina/project-oyster-oa/Haws/bismark-2/multiqc_data/\n", "Reusing existing connection to gannet.fish.washington.edu:443.\n", "HTTP request sent, awaiting response... 200 OK\n", "Length: 2171 (2.1K) [text/html]\n", "Saving to: ‘./index.html.tmp’\n", "\n", "index.html.tmp 100%[===================>] 2.12K --.-KB/s in 0s \n", "\n", "2021-05-17 20:50:31 (2.02 GB/s) - ‘./index.html.tmp’ saved [2171/2171]\n", "\n", "Removing ./index.html.tmp since it should be rejected.\n", "\n", "--2021-05-17 20:50:31-- https://gannet.fish.washington.edu/spartina/project-oyster-oa/Haws/bismark-2/multiqc_report.html\n", "Reusing existing connection to gannet.fish.washington.edu:443.\n", "HTTP request sent, awaiting response... 200 OK\n", "Length: 1448633 (1.4M) [text/html]\n", "Saving to: ‘./multiqc_report.html.tmp’\n", "\n", "multiqc_report.html 100%[===================>] 1.38M --.-KB/s in 0.03s \n", "\n", "2021-05-17 20:50:31 (50.3 MB/s) - ‘./multiqc_report.html.tmp’ saved [1448633/1448633]\n", "\n", "Removing ./multiqc_report.html.tmp since it should be rejected.\n", "\n", "--2021-05-17 20:50:31-- https://gannet.fish.washington.edu/spartina/project-oyster-oa/Haws/bismark-2/zr3644_1_R1_val_1_val_1_val_1_bismark_bt2_PE_report.html\n", "Reusing existing connection to gannet.fish.washington.edu:443.\n", "HTTP request sent, awaiting response... 200 OK\n", "Length: 3162787 (3.0M) [text/html]\n", "Saving to: ‘./zr3644_1_R1_val_1_val_1_val_1_bismark_bt2_PE_report.html.tmp’\n", "\n", "zr3644_1_R1_val_1_v 100%[===================>] 3.02M --.-KB/s in 0.05s \n", "\n", "2021-05-17 20:50:31 (59.3 MB/s) - ‘./zr3644_1_R1_val_1_val_1_val_1_bismark_bt2_PE_report.html.tmp’ saved [3162787/3162787]\n", "\n", "Removing ./zr3644_1_R1_val_1_val_1_val_1_bismark_bt2_PE_report.html.tmp since it should be rejected.\n", "\n", "--2021-05-17 20:50:31-- https://gannet.fish.washington.edu/spartina/project-oyster-oa/Haws/bismark-2/zr3644_1_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph\n", "Reusing existing connection to gannet.fish.washington.edu:443.\n", "HTTP request sent, awaiting response... 200 OK\n", "Length: 238066536 (227M)\n", "Saving to: ‘./zr3644_1_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph’\n", "\n", "zr3644_1_R1_val_1_v 100%[===================>] 227.04M 77.0MB/s in 2.9s \n", "\n", "2021-05-17 20:50:34 (77.0 MB/s) - ‘./zr3644_1_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph’ saved [238066536/238066536]\n", "\n", "--2021-05-17 20:50:34-- https://gannet.fish.washington.edu/spartina/project-oyster-oa/Haws/bismark-2/zr3644_2_R1_val_1_val_1_val_1_bismark_bt2_PE_report.html\n", "Reusing existing connection to gannet.fish.washington.edu:443.\n", "HTTP request sent, awaiting response... 200 OK\n", "Length: 3162899 (3.0M) [text/html]\n", "Saving to: ‘./zr3644_2_R1_val_1_val_1_val_1_bismark_bt2_PE_report.html.tmp’\n", "\n", "zr3644_2_R1_val_1_v 100%[===================>] 3.02M --.-KB/s in 0.1s \n", "\n", "2021-05-17 20:50:34 (31.0 MB/s) - ‘./zr3644_2_R1_val_1_val_1_val_1_bismark_bt2_PE_report.html.tmp’ saved [3162899/3162899]\n", "\n", "Removing ./zr3644_2_R1_val_1_val_1_val_1_bismark_bt2_PE_report.html.tmp since it should be rejected.\n", "\n", "--2021-05-17 20:50:34-- https://gannet.fish.washington.edu/spartina/project-oyster-oa/Haws/bismark-2/zr3644_2_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph\n", "Reusing existing connection to gannet.fish.washington.edu:443.\n", "HTTP request sent, awaiting response... 200 OK\n", "Length: 259414417 (247M)\n", "Saving to: ‘./zr3644_2_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph’\n", "\n", "zr3644_2_R1_val_1_v 100%[===================>] 247.40M 70.3MB/s in 3.5s \n", "\n", "2021-05-17 20:50:38 (70.3 MB/s) - ‘./zr3644_2_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph’ saved [259414417/259414417]\n", "\n", "--2021-05-17 20:50:38-- https://gannet.fish.washington.edu/spartina/project-oyster-oa/Haws/bismark-2/zr3644_3_R1_val_1_val_1_val_1_bismark_bt2_PE_report.html\n", "Reusing existing connection to gannet.fish.washington.edu:443.\n", "HTTP request sent, awaiting response... 200 OK\n", "Length: 3162848 (3.0M) [text/html]\n", "Saving to: ‘./zr3644_3_R1_val_1_val_1_val_1_bismark_bt2_PE_report.html.tmp’\n", "\n", "zr3644_3_R1_val_1_v 100%[===================>] 3.02M --.-KB/s in 0.09s \n", "\n", "2021-05-17 20:50:38 (32.2 MB/s) - ‘./zr3644_3_R1_val_1_val_1_val_1_bismark_bt2_PE_report.html.tmp’ saved [3162848/3162848]\n", "\n", "Removing ./zr3644_3_R1_val_1_val_1_val_1_bismark_bt2_PE_report.html.tmp since it should be rejected.\n", "\n", "--2021-05-17 20:50:38-- https://gannet.fish.washington.edu/spartina/project-oyster-oa/Haws/bismark-2/zr3644_3_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph\n", "Reusing existing connection to gannet.fish.washington.edu:443.\n", "HTTP request sent, awaiting response... 200 OK\n", "Length: 213140550 (203M)\n", "Saving to: ‘./zr3644_3_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph’\n", "\n", "zr3644_3_R1_val_1_v 100%[===================>] 203.27M 75.6MB/s in 2.7s \n", "\n", "2021-05-17 20:50:41 (75.6 MB/s) - ‘./zr3644_3_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph’ saved [213140550/213140550]\n", "\n", "--2021-05-17 20:50:41-- https://gannet.fish.washington.edu/spartina/project-oyster-oa/Haws/bismark-2/zr3644_4_R1_val_1_val_1_val_1_bismark_bt2_PE_report.html\n", "Reusing existing connection to gannet.fish.washington.edu:443.\n", "HTTP request sent, awaiting response... 200 OK\n", "Length: 3162857 (3.0M) [text/html]\n", "Saving to: ‘./zr3644_4_R1_val_1_val_1_val_1_bismark_bt2_PE_report.html.tmp’\n", "\n", "zr3644_4_R1_val_1_v 100%[===================>] 3.02M 19.9MB/s in 0.2s \n", "\n", "2021-05-17 20:50:41 (19.9 MB/s) - ‘./zr3644_4_R1_val_1_val_1_val_1_bismark_bt2_PE_report.html.tmp’ saved [3162857/3162857]\n", "\n", "Removing ./zr3644_4_R1_val_1_val_1_val_1_bismark_bt2_PE_report.html.tmp since it should be rejected.\n", "\n", "--2021-05-17 20:50:41-- https://gannet.fish.washington.edu/spartina/project-oyster-oa/Haws/bismark-2/zr3644_4_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph\n", "Reusing existing connection to gannet.fish.washington.edu:443.\n", "HTTP request sent, awaiting response... 200 OK\n", "Length: 246432525 (235M)\n", "Saving to: ‘./zr3644_4_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph’\n", "\n", "zr3644_4_R1_val_1_v 100%[===================>] 235.02M 68.8MB/s in 3.5s \n", "\n", "2021-05-17 20:50:45 (67.5 MB/s) - ‘./zr3644_4_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph’ saved [246432525/246432525]\n", "\n", "--2021-05-17 20:50:45-- https://gannet.fish.washington.edu/spartina/project-oyster-oa/Haws/bismark-2/zr3644_5_R1_val_1_val_1_val_1_bismark_bt2_PE_report.html\n", "Reusing existing connection to gannet.fish.washington.edu:443.\n", "HTTP request sent, awaiting response... 200 OK\n", "Length: 3162890 (3.0M) [text/html]\n", "Saving to: ‘./zr3644_5_R1_val_1_val_1_val_1_bismark_bt2_PE_report.html.tmp’\n", "\n", "zr3644_5_R1_val_1_v 100%[===================>] 3.02M 17.1MB/s in 0.2s \n", "\n", "2021-05-17 20:50:45 (17.1 MB/s) - ‘./zr3644_5_R1_val_1_val_1_val_1_bismark_bt2_PE_report.html.tmp’ saved [3162890/3162890]\n", "\n", "Removing ./zr3644_5_R1_val_1_val_1_val_1_bismark_bt2_PE_report.html.tmp since it should be rejected.\n", "\n", "--2021-05-17 20:50:45-- https://gannet.fish.washington.edu/spartina/project-oyster-oa/Haws/bismark-2/zr3644_5_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph\n", "Reusing existing connection to gannet.fish.washington.edu:443.\n", "HTTP request sent, awaiting response... 200 OK\n", "Length: 231531553 (221M)\n", "Saving to: ‘./zr3644_5_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph’\n", "\n", "zr3644_5_R1_val_1_v 100%[===================>] 220.81M 77.3MB/s in 2.9s \n", "\n", "2021-05-17 20:50:48 (77.3 MB/s) - ‘./zr3644_5_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph’ saved [231531553/231531553]\n", "\n", "--2021-05-17 20:50:48-- https://gannet.fish.washington.edu/spartina/project-oyster-oa/Haws/bismark-2/zr3644_6_R1_val_1_val_1_val_1_bismark_bt2_PE_report.html\n", "Reusing existing connection to gannet.fish.washington.edu:443.\n", "HTTP request sent, awaiting response... 200 OK\n", "Length: 3162907 (3.0M) [text/html]\n", "Saving to: ‘./zr3644_6_R1_val_1_val_1_val_1_bismark_bt2_PE_report.html.tmp’\n", "\n", "zr3644_6_R1_val_1_v 100%[===================>] 3.02M --.-KB/s in 0.1s \n", "\n", "2021-05-17 20:50:49 (24.0 MB/s) - ‘./zr3644_6_R1_val_1_val_1_val_1_bismark_bt2_PE_report.html.tmp’ saved [3162907/3162907]\n", "\n", "Removing ./zr3644_6_R1_val_1_val_1_val_1_bismark_bt2_PE_report.html.tmp since it should be rejected.\n", "\n", "--2021-05-17 20:50:49-- https://gannet.fish.washington.edu/spartina/project-oyster-oa/Haws/bismark-2/zr3644_6_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph\n", "Reusing existing connection to gannet.fish.washington.edu:443.\n", "HTTP request sent, awaiting response... 200 OK\n", "Length: 255016574 (243M)\n", "Saving to: ‘./zr3644_6_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph’\n", "\n", "zr3644_6_R1_val_1_v 100%[===================>] 243.20M 76.5MB/s in 3.2s \n", "\n", "2021-05-17 20:50:52 (76.5 MB/s) - ‘./zr3644_6_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph’ saved [255016574/255016574]\n", "\n", "--2021-05-17 20:50:52-- https://gannet.fish.washington.edu/spartina/project-oyster-oa/Haws/bismark-2/zr3644_7_R1_val_1_val_1_val_1_bismark_bt2_PE_report.html\n", "Reusing existing connection to gannet.fish.washington.edu:443.\n", "HTTP request sent, awaiting response... 200 OK\n", "Length: 3163096 (3.0M) [text/html]\n", "Saving to: ‘./zr3644_7_R1_val_1_val_1_val_1_bismark_bt2_PE_report.html.tmp’\n", "\n", "zr3644_7_R1_val_1_v 100%[===================>] 3.02M --.-KB/s in 0.07s \n", "\n", "2021-05-17 20:50:52 (42.7 MB/s) - ‘./zr3644_7_R1_val_1_val_1_val_1_bismark_bt2_PE_report.html.tmp’ saved [3163096/3163096]\n", "\n", "Removing ./zr3644_7_R1_val_1_val_1_val_1_bismark_bt2_PE_report.html.tmp since it should be rejected.\n", "\n", "--2021-05-17 20:50:52-- https://gannet.fish.washington.edu/spartina/project-oyster-oa/Haws/bismark-2/zr3644_7_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph\n", "Reusing existing connection to gannet.fish.washington.edu:443.\n", "HTTP request sent, awaiting response... 200 OK\n", "Length: 312303076 (298M)\n", "Saving to: ‘./zr3644_7_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph’\n", "\n", "zr3644_7_R1_val_1_v 100%[===================>] 297.83M 76.8MB/s in 3.9s \n", "\n", "2021-05-17 20:50:56 (75.9 MB/s) - ‘./zr3644_7_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph’ saved [312303076/312303076]\n", "\n", "--2021-05-17 20:50:56-- https://gannet.fish.washington.edu/spartina/project-oyster-oa/Haws/bismark-2/zr3644_8_R1_val_1_val_1_val_1_bismark_bt2_PE_report.html\n", "Reusing existing connection to gannet.fish.washington.edu:443.\n", "HTTP request sent, awaiting response... 200 OK\n", "Length: 3162893 (3.0M) [text/html]\n", "Saving to: ‘./zr3644_8_R1_val_1_val_1_val_1_bismark_bt2_PE_report.html.tmp’\n", "\n", "zr3644_8_R1_val_1_v 100%[===================>] 3.02M --.-KB/s in 0.06s \n", "\n", "2021-05-17 20:50:57 (48.8 MB/s) - ‘./zr3644_8_R1_val_1_val_1_val_1_bismark_bt2_PE_report.html.tmp’ saved [3162893/3162893]\n", "\n", "Removing ./zr3644_8_R1_val_1_val_1_val_1_bismark_bt2_PE_report.html.tmp since it should be rejected.\n", "\n", "--2021-05-17 20:50:57-- https://gannet.fish.washington.edu/spartina/project-oyster-oa/Haws/bismark-2/zr3644_8_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph\n", "Reusing existing connection to gannet.fish.washington.edu:443.\n", "HTTP request sent, awaiting response... 200 OK\n", "Length: 223070567 (213M)\n", "Saving to: ‘./zr3644_8_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph’\n", "\n", "zr3644_8_R1_val_1_v 100%[===================>] 212.74M 82.8MB/s in 2.6s \n", "\n", "2021-05-17 20:50:59 (82.8 MB/s) - ‘./zr3644_8_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph’ saved [223070567/223070567]\n", "\n", "--2021-05-17 20:50:59-- https://gannet.fish.washington.edu/spartina/project-oyster-oa/Haws/bismark-2/zr3644_9_R1_val_1_val_1_val_1_bismark_bt2_PE_report.html\n", "Reusing existing connection to gannet.fish.washington.edu:443.\n", "HTTP request sent, awaiting response... 200 OK\n", "Length: 3162880 (3.0M) [text/html]\n", "Saving to: ‘./zr3644_9_R1_val_1_val_1_val_1_bismark_bt2_PE_report.html.tmp’\n", "\n", "zr3644_9_R1_val_1_v 100%[===================>] 3.02M --.-KB/s in 0.07s \n", "\n", "2021-05-17 20:51:00 (42.7 MB/s) - ‘./zr3644_9_R1_val_1_val_1_val_1_bismark_bt2_PE_report.html.tmp’ saved [3162880/3162880]\n", "\n", "Removing ./zr3644_9_R1_val_1_val_1_val_1_bismark_bt2_PE_report.html.tmp since it should be rejected.\n", "\n", "--2021-05-17 20:51:00-- https://gannet.fish.washington.edu/spartina/project-oyster-oa/Haws/bismark-2/zr3644_9_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph\n", "Reusing existing connection to gannet.fish.washington.edu:443.\n", "HTTP request sent, awaiting response... 200 OK\n", "Length: 228264905 (218M)\n", "Saving to: ‘./zr3644_9_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph’\n", "\n", "zr3644_9_R1_val_1_v 100%[===================>] 217.69M 83.9MB/s in 2.6s \n", "\n", "2021-05-17 20:51:02 (83.9 MB/s) - ‘./zr3644_9_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph’ saved [228264905/228264905]\n", "\n", "--2021-05-17 20:51:02-- https://gannet.fish.washington.edu/spartina/project-oyster-oa/Haws/bismark-2/zr3644_10_R1_val_1_val_1_val_1_bismark_bt2_PE_report.html\n", "Reusing existing connection to gannet.fish.washington.edu:443.\n", "HTTP request sent, awaiting response... 200 OK\n", "Length: 3162948 (3.0M) [text/html]\n", "Saving to: ‘./zr3644_10_R1_val_1_val_1_val_1_bismark_bt2_PE_report.html.tmp’\n", "\n", "zr3644_10_R1_val_1_ 100%[===================>] 3.02M --.-KB/s in 0.07s \n", "\n", "2021-05-17 20:51:03 (41.1 MB/s) - ‘./zr3644_10_R1_val_1_val_1_val_1_bismark_bt2_PE_report.html.tmp’ saved [3162948/3162948]\n", "\n", "Removing ./zr3644_10_R1_val_1_val_1_val_1_bismark_bt2_PE_report.html.tmp since it should be rejected.\n", "\n", "--2021-05-17 20:51:03-- https://gannet.fish.washington.edu/spartina/project-oyster-oa/Haws/bismark-2/zr3644_10_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph\n", "Reusing existing connection to gannet.fish.washington.edu:443.\n", "HTTP request sent, awaiting response... 200 OK\n", "Length: 251375395 (240M)\n", "Saving to: ‘./zr3644_10_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph’\n", "\n", "zr3644_10_R1_val_1_ 100%[===================>] 239.73M 78.6MB/s in 3.1s \n", "\n", "2021-05-17 20:51:06 (78.6 MB/s) - ‘./zr3644_10_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph’ saved [251375395/251375395]\n", "\n", "--2021-05-17 20:51:06-- https://gannet.fish.washington.edu/spartina/project-oyster-oa/Haws/bismark-2/zr3644_11_R1_val_1_val_1_val_1_bismark_bt2_PE_report.html\n", "Reusing existing connection to gannet.fish.washington.edu:443.\n", "HTTP request sent, awaiting response... 200 OK\n", "Length: 3162937 (3.0M) [text/html]\n", "Saving to: ‘./zr3644_11_R1_val_1_val_1_val_1_bismark_bt2_PE_report.html.tmp’\n", "\n", "zr3644_11_R1_val_1_ 100%[===================>] 3.02M --.-KB/s in 0.09s \n", "\n", "2021-05-17 20:51:06 (34.2 MB/s) - ‘./zr3644_11_R1_val_1_val_1_val_1_bismark_bt2_PE_report.html.tmp’ saved [3162937/3162937]\n", "\n", "Removing ./zr3644_11_R1_val_1_val_1_val_1_bismark_bt2_PE_report.html.tmp since it should be rejected.\n", "\n", "--2021-05-17 20:51:06-- https://gannet.fish.washington.edu/spartina/project-oyster-oa/Haws/bismark-2/zr3644_11_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph\n", "Reusing existing connection to gannet.fish.washington.edu:443.\n", "HTTP request sent, awaiting response... 200 OK\n", "Length: 263423261 (251M)\n", "Saving to: ‘./zr3644_11_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph’\n", "\n", "zr3644_11_R1_val_1_ 100%[===================>] 251.22M 78.4MB/s in 3.3s \n", "\n", "2021-05-17 20:51:09 (75.5 MB/s) - ‘./zr3644_11_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph’ saved [263423261/263423261]\n", "\n", "--2021-05-17 20:51:10-- https://gannet.fish.washington.edu/spartina/project-oyster-oa/Haws/bismark-2/zr3644_12_R1_val_1_val_1_val_1_bismark_bt2_PE_report.html\n", "Reusing existing connection to gannet.fish.washington.edu:443.\n", "HTTP request sent, awaiting response... 200 OK\n", "Length: 3162813 (3.0M) [text/html]\n", "Saving to: ‘./zr3644_12_R1_val_1_val_1_val_1_bismark_bt2_PE_report.html.tmp’\n", "\n", "zr3644_12_R1_val_1_ 100%[===================>] 3.02M --.-KB/s in 0.05s \n", "\n", "2021-05-17 20:51:10 (61.0 MB/s) - ‘./zr3644_12_R1_val_1_val_1_val_1_bismark_bt2_PE_report.html.tmp’ saved [3162813/3162813]\n", "\n", "Removing ./zr3644_12_R1_val_1_val_1_val_1_bismark_bt2_PE_report.html.tmp since it should be rejected.\n", "\n", "--2021-05-17 20:51:10-- https://gannet.fish.washington.edu/spartina/project-oyster-oa/Haws/bismark-2/zr3644_12_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph\n", "Reusing existing connection to gannet.fish.washington.edu:443.\n", "HTTP request sent, awaiting response... 200 OK\n", "Length: 238209851 (227M)\n", "Saving to: ‘./zr3644_12_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph’\n", "\n", "zr3644_12_R1_val_1_ 100%[===================>] 227.17M 74.1MB/s in 3.1s \n", "\n", "2021-05-17 20:51:13 (74.1 MB/s) - ‘./zr3644_12_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph’ saved [238209851/238209851]\n", "\n", "--2021-05-17 20:51:13-- https://gannet.fish.washington.edu/spartina/project-oyster-oa/Haws/bismark-2/zr3644_13_R1_val_1_val_1_val_1_bismark_bt2_PE_report.html\n", "Reusing existing connection to gannet.fish.washington.edu:443.\n", "HTTP request sent, awaiting response... 200 OK\n", "Length: 3162939 (3.0M) [text/html]\n", "Saving to: ‘./zr3644_13_R1_val_1_val_1_val_1_bismark_bt2_PE_report.html.tmp’\n", "\n", "zr3644_13_R1_val_1_ 100%[===================>] 3.02M 19.0MB/s in 0.2s \n", "\n", "2021-05-17 20:51:13 (19.0 MB/s) - ‘./zr3644_13_R1_val_1_val_1_val_1_bismark_bt2_PE_report.html.tmp’ saved [3162939/3162939]\n", "\n", "Removing ./zr3644_13_R1_val_1_val_1_val_1_bismark_bt2_PE_report.html.tmp since it should be rejected.\n", "\n", "--2021-05-17 20:51:13-- https://gannet.fish.washington.edu/spartina/project-oyster-oa/Haws/bismark-2/zr3644_13_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph\n", "Reusing existing connection to gannet.fish.washington.edu:443.\n", "HTTP request sent, awaiting response... 200 OK\n", "Length: 259038737 (247M)\n", "Saving to: ‘./zr3644_13_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph’\n", "\n", "zr3644_13_R1_val_1_ 100%[===================>] 247.04M 77.7MB/s in 3.3s \n", "\n", "2021-05-17 20:51:17 (75.7 MB/s) - ‘./zr3644_13_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph’ saved [259038737/259038737]\n", "\n", "--2021-05-17 20:51:17-- https://gannet.fish.washington.edu/spartina/project-oyster-oa/Haws/bismark-2/zr3644_14_R1_val_1_val_1_val_1_bismark_bt2_PE_report.html\n", "Reusing existing connection to gannet.fish.washington.edu:443.\n", "HTTP request sent, awaiting response... 200 OK\n", "Length: 3162943 (3.0M) [text/html]\n", "Saving to: ‘./zr3644_14_R1_val_1_val_1_val_1_bismark_bt2_PE_report.html.tmp’\n", "\n", "zr3644_14_R1_val_1_ 100%[===================>] 3.02M --.-KB/s in 0.1s \n", "\n", "2021-05-17 20:51:17 (21.0 MB/s) - ‘./zr3644_14_R1_val_1_val_1_val_1_bismark_bt2_PE_report.html.tmp’ saved [3162943/3162943]\n", "\n", "Removing ./zr3644_14_R1_val_1_val_1_val_1_bismark_bt2_PE_report.html.tmp since it should be rejected.\n", "\n", "--2021-05-17 20:51:17-- https://gannet.fish.washington.edu/spartina/project-oyster-oa/Haws/bismark-2/zr3644_14_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph\n", "Reusing existing connection to gannet.fish.washington.edu:443.\n", "HTTP request sent, awaiting response... 200 OK\n", "Length: 200672316 (191M)\n", "Saving to: ‘./zr3644_14_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph’\n", "\n", "zr3644_14_R1_val_1_ 100%[===================>] 191.38M 77.1MB/s in 2.5s \n", "\n", "2021-05-17 20:51:20 (77.1 MB/s) - ‘./zr3644_14_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph’ saved [200672316/200672316]\n", "\n", "--2021-05-17 20:51:20-- https://gannet.fish.washington.edu/spartina/project-oyster-oa/Haws/bismark-2/zr3644_15_R1_val_1_val_1_val_1_bismark_bt2_PE_report.html\n", "Reusing existing connection to gannet.fish.washington.edu:443.\n", "HTTP request sent, awaiting response... 200 OK\n", "Length: 3163012 (3.0M) [text/html]\n", "Saving to: ‘./zr3644_15_R1_val_1_val_1_val_1_bismark_bt2_PE_report.html.tmp’\n", "\n", "zr3644_15_R1_val_1_ 100%[===================>] 3.02M 13.4MB/s in 0.2s \n", "\n", "2021-05-17 20:51:20 (13.4 MB/s) - ‘./zr3644_15_R1_val_1_val_1_val_1_bismark_bt2_PE_report.html.tmp’ saved [3163012/3163012]\n", "\n", "Removing ./zr3644_15_R1_val_1_val_1_val_1_bismark_bt2_PE_report.html.tmp since it should be rejected.\n", "\n", "--2021-05-17 20:51:20-- https://gannet.fish.washington.edu/spartina/project-oyster-oa/Haws/bismark-2/zr3644_15_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph\n", "Reusing existing connection to gannet.fish.washington.edu:443.\n", "HTTP request sent, awaiting response... 200 OK\n", "Length: 270532466 (258M)\n", "Saving to: ‘./zr3644_15_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph’\n", "\n", "zr3644_15_R1_val_1_ 100%[===================>] 258.00M 78.3MB/s in 3.4s \n", "\n", "2021-05-17 20:51:23 (75.8 MB/s) - ‘./zr3644_15_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph’ saved [270532466/270532466]\n", "\n", "--2021-05-17 20:51:24-- https://gannet.fish.washington.edu/spartina/project-oyster-oa/Haws/bismark-2/zr3644_16_R1_val_1_val_1_val_1_bismark_bt2_PE_report.html\n", "Reusing existing connection to gannet.fish.washington.edu:443.\n", "HTTP request sent, awaiting response... 200 OK\n", "Length: 3162888 (3.0M) [text/html]\n", "Saving to: ‘./zr3644_16_R1_val_1_val_1_val_1_bismark_bt2_PE_report.html.tmp’\n", "\n", "zr3644_16_R1_val_1_ 100%[===================>] 3.02M --.-KB/s in 0.1s \n", "\n", "2021-05-17 20:51:24 (27.9 MB/s) - ‘./zr3644_16_R1_val_1_val_1_val_1_bismark_bt2_PE_report.html.tmp’ saved [3162888/3162888]\n", "\n", "Removing ./zr3644_16_R1_val_1_val_1_val_1_bismark_bt2_PE_report.html.tmp since it should be rejected.\n", "\n", "--2021-05-17 20:51:24-- https://gannet.fish.washington.edu/spartina/project-oyster-oa/Haws/bismark-2/zr3644_16_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph\n", "Reusing existing connection to gannet.fish.washington.edu:443.\n", "HTTP request sent, awaiting response... 200 OK\n", "Length: 237862261 (227M)\n", "Saving to: ‘./zr3644_16_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph’\n", "\n", "zr3644_16_R1_val_1_ 100%[===================>] 226.84M 74.9MB/s in 3.0s \n", "\n", "2021-05-17 20:51:27 (74.9 MB/s) - ‘./zr3644_16_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph’ saved [237862261/237862261]\n", "\n", "--2021-05-17 20:51:27-- https://gannet.fish.washington.edu/spartina/project-oyster-oa/Haws/bismark-2/zr3644_17_R1_val_1_val_1_val_1_bismark_bt2_PE_report.html\n", "Reusing existing connection to gannet.fish.washington.edu:443.\n", "HTTP request sent, awaiting response... 200 OK\n", "Length: 3162911 (3.0M) [text/html]\n", "Saving to: ‘./zr3644_17_R1_val_1_val_1_val_1_bismark_bt2_PE_report.html.tmp’\n", "\n", "zr3644_17_R1_val_1_ 100%[===================>] 3.02M --.-KB/s in 0.07s \n", "\n", "2021-05-17 20:51:27 (45.3 MB/s) - ‘./zr3644_17_R1_val_1_val_1_val_1_bismark_bt2_PE_report.html.tmp’ saved [3162911/3162911]\n", "\n", "Removing ./zr3644_17_R1_val_1_val_1_val_1_bismark_bt2_PE_report.html.tmp since it should be rejected.\n", "\n", "--2021-05-17 20:51:27-- https://gannet.fish.washington.edu/spartina/project-oyster-oa/Haws/bismark-2/zr3644_17_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph\n", "Reusing existing connection to gannet.fish.washington.edu:443.\n", "HTTP request sent, awaiting response... 200 OK\n", "Length: 255762365 (244M)\n", "Saving to: ‘./zr3644_17_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph’\n", "\n", "zr3644_17_R1_val_1_ 100%[===================>] 243.91M 78.2MB/s in 3.1s \n", "\n", "2021-05-17 20:51:30 (78.2 MB/s) - ‘./zr3644_17_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph’ saved [255762365/255762365]\n", "\n", "--2021-05-17 20:51:31-- https://gannet.fish.washington.edu/spartina/project-oyster-oa/Haws/bismark-2/zr3644_18_R1_val_1_val_1_val_1_bismark_bt2_PE_report.html\n", "Reusing existing connection to gannet.fish.washington.edu:443.\n", "HTTP request sent, awaiting response... 200 OK\n", "Length: 3162932 (3.0M) [text/html]\n", "Saving to: ‘./zr3644_18_R1_val_1_val_1_val_1_bismark_bt2_PE_report.html.tmp’\n", "\n", "zr3644_18_R1_val_1_ 100%[===================>] 3.02M --.-KB/s in 0.1s \n", "\n", "2021-05-17 20:51:31 (26.6 MB/s) - ‘./zr3644_18_R1_val_1_val_1_val_1_bismark_bt2_PE_report.html.tmp’ saved [3162932/3162932]\n", "\n", "Removing ./zr3644_18_R1_val_1_val_1_val_1_bismark_bt2_PE_report.html.tmp since it should be rejected.\n", "\n", "--2021-05-17 20:51:31-- https://gannet.fish.washington.edu/spartina/project-oyster-oa/Haws/bismark-2/zr3644_18_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph\n", "Reusing existing connection to gannet.fish.washington.edu:443.\n", "HTTP request sent, awaiting response... 200 OK\n", "Length: 246151472 (235M)\n", "Saving to: ‘./zr3644_18_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph’\n", "\n", "zr3644_18_R1_val_1_ 100%[===================>] 234.75M 73.9MB/s in 3.2s \n", "\n", "2021-05-17 20:51:34 (73.8 MB/s) - ‘./zr3644_18_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph’ saved [246151472/246151472]\n", "\n", "--2021-05-17 20:51:34-- https://gannet.fish.washington.edu/spartina/project-oyster-oa/Haws/bismark-2/zr3644_19_R1_val_1_val_1_val_1_bismark_bt2_PE_report.html\n", "Reusing existing connection to gannet.fish.washington.edu:443.\n", "HTTP request sent, awaiting response... 200 OK\n", "Length: 3162886 (3.0M) [text/html]\n", "Saving to: ‘./zr3644_19_R1_val_1_val_1_val_1_bismark_bt2_PE_report.html.tmp’\n", "\n", "zr3644_19_R1_val_1_ 100%[===================>] 3.02M --.-KB/s in 0.07s \n", "\n", "2021-05-17 20:51:34 (45.6 MB/s) - ‘./zr3644_19_R1_val_1_val_1_val_1_bismark_bt2_PE_report.html.tmp’ saved [3162886/3162886]\n", "\n", "Removing ./zr3644_19_R1_val_1_val_1_val_1_bismark_bt2_PE_report.html.tmp since it should be rejected.\n", "\n", "--2021-05-17 20:51:34-- https://gannet.fish.washington.edu/spartina/project-oyster-oa/Haws/bismark-2/zr3644_19_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph\n", "Reusing existing connection to gannet.fish.washington.edu:443.\n", "HTTP request sent, awaiting response... 200 OK\n", "Length: 243551222 (232M)\n", "Saving to: ‘./zr3644_19_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph’\n", "\n", "zr3644_19_R1_val_1_ 100%[===================>] 232.27M 75.2MB/s in 3.1s \n", "\n", "2021-05-17 20:51:37 (75.2 MB/s) - ‘./zr3644_19_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph’ saved [243551222/243551222]\n", "\n", "--2021-05-17 20:51:38-- https://gannet.fish.washington.edu/spartina/project-oyster-oa/Haws/bismark-2/zr3644_20_R1_val_1_val_1_val_1_bismark_bt2_PE_report.html\n", "Reusing existing connection to gannet.fish.washington.edu:443.\n", "HTTP request sent, awaiting response... 200 OK\n", "Length: 3162920 (3.0M) [text/html]\n", "Saving to: ‘./zr3644_20_R1_val_1_val_1_val_1_bismark_bt2_PE_report.html.tmp’\n", "\n", "zr3644_20_R1_val_1_ 100%[===================>] 3.02M --.-KB/s in 0.04s \n", "\n", "2021-05-17 20:51:38 (72.8 MB/s) - ‘./zr3644_20_R1_val_1_val_1_val_1_bismark_bt2_PE_report.html.tmp’ saved [3162920/3162920]\n", "\n", "Removing ./zr3644_20_R1_val_1_val_1_val_1_bismark_bt2_PE_report.html.tmp since it should be rejected.\n", "\n", "--2021-05-17 20:51:38-- https://gannet.fish.washington.edu/spartina/project-oyster-oa/Haws/bismark-2/zr3644_20_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph\n", "Reusing existing connection to gannet.fish.washington.edu:443.\n", "HTTP request sent, awaiting response... 200 OK\n", "Length: 255785102 (244M)\n", "Saving to: ‘./zr3644_20_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph’\n", "\n", "zr3644_20_R1_val_1_ 100%[===================>] 243.94M 81.8MB/s in 3.0s \n", "\n", "2021-05-17 20:51:41 (81.8 MB/s) - ‘./zr3644_20_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph’ saved [255785102/255785102]\n", "\n", "--2021-05-17 20:51:41-- https://gannet.fish.washington.edu/spartina/project-oyster-oa/Haws/bismark-2/zr3644_21_R1_val_1_val_1_val_1_bismark_bt2_PE_report.html\n", "Reusing existing connection to gannet.fish.washington.edu:443.\n", "HTTP request sent, awaiting response... 200 OK\n", "Length: 3162929 (3.0M) [text/html]\n", "Saving to: ‘./zr3644_21_R1_val_1_val_1_val_1_bismark_bt2_PE_report.html.tmp’\n", "\n", "zr3644_21_R1_val_1_ 100%[===================>] 3.02M --.-KB/s in 0.06s \n", "\n", "2021-05-17 20:51:41 (48.0 MB/s) - ‘./zr3644_21_R1_val_1_val_1_val_1_bismark_bt2_PE_report.html.tmp’ saved [3162929/3162929]\n", "\n", "Removing ./zr3644_21_R1_val_1_val_1_val_1_bismark_bt2_PE_report.html.tmp since it should be rejected.\n", "\n", "--2021-05-17 20:51:41-- https://gannet.fish.washington.edu/spartina/project-oyster-oa/Haws/bismark-2/zr3644_21_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph\n", "Reusing existing connection to gannet.fish.washington.edu:443.\n", "HTTP request sent, awaiting response... 200 OK\n", "Length: 251936294 (240M)\n", "Saving to: ‘./zr3644_21_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph’\n", "\n", "zr3644_21_R1_val_1_ 100%[===================>] 240.26M 66.9MB/s in 3.5s \n", "\n", "2021-05-17 20:51:45 (68.9 MB/s) - ‘./zr3644_21_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph’ saved [251936294/251936294]\n", "\n", "--2021-05-17 20:51:45-- https://gannet.fish.washington.edu/spartina/project-oyster-oa/Haws/bismark-2/zr3644_22_R1_val_1_val_1_val_1_bismark_bt2_PE_report.html\n", "Reusing existing connection to gannet.fish.washington.edu:443.\n", "HTTP request sent, awaiting response... 200 OK\n", "Length: 3162894 (3.0M) [text/html]\n", "Saving to: ‘./zr3644_22_R1_val_1_val_1_val_1_bismark_bt2_PE_report.html.tmp’\n", "\n", "zr3644_22_R1_val_1_ 100%[===================>] 3.02M 19.9MB/s in 0.2s \n", "\n", "2021-05-17 20:51:45 (19.9 MB/s) - ‘./zr3644_22_R1_val_1_val_1_val_1_bismark_bt2_PE_report.html.tmp’ saved [3162894/3162894]\n", "\n", "Removing ./zr3644_22_R1_val_1_val_1_val_1_bismark_bt2_PE_report.html.tmp since it should be rejected.\n", "\n", "--2021-05-17 20:51:45-- https://gannet.fish.washington.edu/spartina/project-oyster-oa/Haws/bismark-2/zr3644_22_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph\n", "Reusing existing connection to gannet.fish.washington.edu:443.\n", "HTTP request sent, awaiting response... 200 OK\n", "Length: 236205711 (225M)\n", "Saving to: ‘./zr3644_22_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph’\n", "\n", "zr3644_22_R1_val_1_ 100%[===================>] 225.26M 77.7MB/s in 2.9s \n", "\n", "2021-05-17 20:51:48 (77.7 MB/s) - ‘./zr3644_22_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph’ saved [236205711/236205711]\n", "\n", "--2021-05-17 20:51:48-- https://gannet.fish.washington.edu/spartina/project-oyster-oa/Haws/bismark-2/zr3644_23_R1_val_1_val_1_val_1_bismark_bt2_PE_report.html\n", "Reusing existing connection to gannet.fish.washington.edu:443.\n", "HTTP request sent, awaiting response... 200 OK\n", "Length: 3162830 (3.0M) [text/html]\n", "Saving to: ‘./zr3644_23_R1_val_1_val_1_val_1_bismark_bt2_PE_report.html.tmp’\n", "\n", "zr3644_23_R1_val_1_ 100%[===================>] 3.02M --.-KB/s in 0.06s \n", "\n", "2021-05-17 20:51:48 (50.5 MB/s) - ‘./zr3644_23_R1_val_1_val_1_val_1_bismark_bt2_PE_report.html.tmp’ saved [3162830/3162830]\n", "\n", "Removing ./zr3644_23_R1_val_1_val_1_val_1_bismark_bt2_PE_report.html.tmp since it should be rejected.\n", "\n", "--2021-05-17 20:51:48-- https://gannet.fish.washington.edu/spartina/project-oyster-oa/Haws/bismark-2/zr3644_23_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph\n", "Reusing existing connection to gannet.fish.washington.edu:443.\n", "HTTP request sent, awaiting response... 200 OK\n", "Length: 210792563 (201M)\n", "Saving to: ‘./zr3644_23_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph’\n", "\n", "zr3644_23_R1_val_1_ 100%[===================>] 201.03M 71.8MB/s in 2.8s \n", "\n", "2021-05-17 20:51:51 (71.8 MB/s) - ‘./zr3644_23_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph’ saved [210792563/210792563]\n", "\n", "--2021-05-17 20:51:51-- https://gannet.fish.washington.edu/spartina/project-oyster-oa/Haws/bismark-2/zr3644_24_R1_val_1_val_1_val_1_bismark_bt2_PE_report.html\n", "Reusing existing connection to gannet.fish.washington.edu:443.\n", "HTTP request sent, awaiting response... 200 OK\n", "Length: 3162911 (3.0M) [text/html]\n", "Saving to: ‘./zr3644_24_R1_val_1_val_1_val_1_bismark_bt2_PE_report.html.tmp’\n", "\n", "zr3644_24_R1_val_1_ 100%[===================>] 3.02M --.-KB/s in 0.1s \n", "\n", "2021-05-17 20:51:51 (22.5 MB/s) - ‘./zr3644_24_R1_val_1_val_1_val_1_bismark_bt2_PE_report.html.tmp’ saved [3162911/3162911]\n", "\n", "Removing ./zr3644_24_R1_val_1_val_1_val_1_bismark_bt2_PE_report.html.tmp since it should be rejected.\n", "\n", "--2021-05-17 20:51:51-- https://gannet.fish.washington.edu/spartina/project-oyster-oa/Haws/bismark-2/zr3644_24_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph\n", "Reusing existing connection to gannet.fish.washington.edu:443.\n", "HTTP request sent, awaiting response... 200 OK\n", "Length: 250700953 (239M)\n", "Saving to: ‘./zr3644_24_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph’\n", "\n", "zr3644_24_R1_val_1_ 100%[===================>] 239.09M 74.8MB/s in 3.3s \n", "\n", "2021-05-17 20:51:55 (72.9 MB/s) - ‘./zr3644_24_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph’ saved [250700953/250700953]\n", "\n", "--2021-05-17 20:51:55-- https://gannet.fish.washington.edu/spartina/project-oyster-oa/Haws/bismark-2/?C=N;O=A\n", "Reusing existing connection to gannet.fish.washington.edu:443.\n", "HTTP request sent, awaiting response... 200 OK\n", "Length: unspecified [text/html]\n", "Saving to: ‘./index.html?C=N;O=A.tmp’\n", "\n", "index.html?C=N;O=A. [ <=> ] 168.69K --.-KB/s in 0.003s \n", "\n", "2021-05-17 20:52:00 (61.0 MB/s) - ‘./index.html?C=N;O=A.tmp’ saved [172743]\n", "\n", "Removing ./index.html?C=N;O=A.tmp since it should be rejected.\n", "\n", "--2021-05-17 20:52:00-- https://gannet.fish.washington.edu/spartina/project-oyster-oa/Haws/bismark-2/?C=M;O=D\n", "Reusing existing connection to gannet.fish.washington.edu:443.\n", "HTTP request sent, awaiting response... 200 OK\n", "Length: unspecified [text/html]\n", "Saving to: ‘./index.html?C=M;O=D.tmp’\n", "\n", "index.html?C=M;O=D. [ <=> ] 168.69K --.-KB/s in 0.004s \n", "\n", "2021-05-17 20:52:04 (39.0 MB/s) - ‘./index.html?C=M;O=D.tmp’ saved [172743]\n", "\n", "Removing ./index.html?C=M;O=D.tmp since it should be rejected.\n", "\n", "--2021-05-17 20:52:04-- https://gannet.fish.washington.edu/spartina/project-oyster-oa/Haws/bismark-2/?C=S;O=D\n", "Reusing existing connection to gannet.fish.washington.edu:443.\n", "HTTP request sent, awaiting response... 200 OK\n", "Length: unspecified [text/html]\n", "Saving to: ‘./index.html?C=S;O=D.tmp’\n", "\n", "index.html?C=S;O=D. [ <=> ] 168.69K --.-KB/s in 0.004s \n", "\n", "2021-05-17 20:52:09 (39.0 MB/s) - ‘./index.html?C=S;O=D.tmp’ saved [172743]\n", "\n", "Removing ./index.html?C=S;O=D.tmp since it should be rejected.\n", "\n", "--2021-05-17 20:52:09-- https://gannet.fish.washington.edu/spartina/project-oyster-oa/Haws/bismark-2/?C=D;O=D\n", "Reusing existing connection to gannet.fish.washington.edu:443.\n", "HTTP request sent, awaiting response... 200 OK\n", "Length: unspecified [text/html]\n", "Saving to: ‘./index.html?C=D;O=D.tmp’\n", "\n", "index.html?C=D;O=D. [ <=> ] 168.69K --.-KB/s in 0.004s \n", "\n", "2021-05-17 20:52:14 (38.8 MB/s) - ‘./index.html?C=D;O=D.tmp’ saved [172743]\n", "\n", "Removing ./index.html?C=D;O=D.tmp since it should be rejected.\n", "\n", "--2021-05-17 20:52:14-- https://gannet.fish.washington.edu/spartina/project-oyster-oa/Haws/bismark-2/multiqc_data/?C=N;O=D\n", "Reusing existing connection to gannet.fish.washington.edu:443.\n", "HTTP request sent, awaiting response... 200 OK\n", "Length: 2171 (2.1K) [text/html]\n", "Saving to: ‘./index.html?C=N;O=D.tmp’\n", "\n", "index.html?C=N;O=D. 100%[===================>] 2.12K --.-KB/s in 0s \n", "\n", "2021-05-17 20:52:14 (2.02 GB/s) - ‘./index.html?C=N;O=D.tmp’ saved [2171/2171]\n", "\n", "Removing ./index.html?C=N;O=D.tmp since it should be rejected.\n", "\n", "--2021-05-17 20:52:14-- https://gannet.fish.washington.edu/spartina/project-oyster-oa/Haws/bismark-2/multiqc_data/?C=M;O=A\n", "Reusing existing connection to gannet.fish.washington.edu:443.\n", "HTTP request sent, awaiting response... 200 OK\n", "Length: 2171 (2.1K) [text/html]\n", "Saving to: ‘./index.html?C=M;O=A.tmp’\n", "\n", "index.html?C=M;O=A. 100%[===================>] 2.12K --.-KB/s in 0s \n", "\n", "2021-05-17 20:52:14 (2.02 GB/s) - ‘./index.html?C=M;O=A.tmp’ saved [2171/2171]\n", "\n", "Removing ./index.html?C=M;O=A.tmp since it should be rejected.\n", "\n", "--2021-05-17 20:52:14-- https://gannet.fish.washington.edu/spartina/project-oyster-oa/Haws/bismark-2/multiqc_data/?C=S;O=A\n", "Reusing existing connection to gannet.fish.washington.edu:443.\n", "HTTP request sent, awaiting response... 200 OK\n", "Length: 2171 (2.1K) [text/html]\n", "Saving to: ‘./index.html?C=S;O=A.tmp’\n", "\n", "index.html?C=S;O=A. 100%[===================>] 2.12K --.-KB/s in 0s \n", "\n", "2021-05-17 20:52:14 (2.02 GB/s) - ‘./index.html?C=S;O=A.tmp’ saved [2171/2171]\n", "\n", "Removing ./index.html?C=S;O=A.tmp since it should be rejected.\n", "\n", "--2021-05-17 20:52:14-- https://gannet.fish.washington.edu/spartina/project-oyster-oa/Haws/bismark-2/multiqc_data/?C=D;O=A\n", "Reusing existing connection to gannet.fish.washington.edu:443.\n", "HTTP request sent, awaiting response... 200 OK\n", "Length: 2171 (2.1K) [text/html]\n", "Saving to: ‘./index.html?C=D;O=A.tmp’\n", "\n", "index.html?C=D;O=A. 100%[===================>] 2.12K --.-KB/s in 0s \n", "\n", "2021-05-17 20:52:14 (2.02 GB/s) - ‘./index.html?C=D;O=A.tmp’ saved [2171/2171]\n", "\n", "Removing ./index.html?C=D;O=A.tmp since it should be rejected.\n", "\n", "--2021-05-17 20:52:14-- https://gannet.fish.washington.edu/spartina/project-oyster-oa/Haws/bismark-2/multiqc_data/?C=N;O=A\n", "Reusing existing connection to gannet.fish.washington.edu:443.\n", "HTTP request sent, awaiting response... 200 OK\n", "Length: 2171 (2.1K) [text/html]\n", "Saving to: ‘./index.html?C=N;O=A.tmp’\n", "\n", "index.html?C=N;O=A. 100%[===================>] 2.12K --.-KB/s in 0s \n", "\n", "2021-05-17 20:52:14 (2.02 GB/s) - ‘./index.html?C=N;O=A.tmp’ saved [2171/2171]\n", "\n", "Removing ./index.html?C=N;O=A.tmp since it should be rejected.\n", "\n", "--2021-05-17 20:52:14-- https://gannet.fish.washington.edu/spartina/project-oyster-oa/Haws/bismark-2/multiqc_data/?C=M;O=D\n", "Reusing existing connection to gannet.fish.washington.edu:443.\n", "HTTP request sent, awaiting response... 200 OK\n", "Length: 2171 (2.1K) [text/html]\n", "Saving to: ‘./index.html?C=M;O=D.tmp’\n", "\n", "index.html?C=M;O=D. 100%[===================>] 2.12K --.-KB/s in 0s \n", "\n", "2021-05-17 20:52:14 (2.02 GB/s) - ‘./index.html?C=M;O=D.tmp’ saved [2171/2171]\n", "\n", "Removing ./index.html?C=M;O=D.tmp since it should be rejected.\n", "\n", "--2021-05-17 20:52:14-- https://gannet.fish.washington.edu/spartina/project-oyster-oa/Haws/bismark-2/multiqc_data/?C=S;O=D\n", "Reusing existing connection to gannet.fish.washington.edu:443.\n", "HTTP request sent, awaiting response... 200 OK\n", "Length: 2171 (2.1K) [text/html]\n", "Saving to: ‘./index.html?C=S;O=D.tmp’\n", "\n", "index.html?C=S;O=D. 100%[===================>] 2.12K --.-KB/s in 0s \n", "\n", "2021-05-17 20:52:14 (2.02 GB/s) - ‘./index.html?C=S;O=D.tmp’ saved [2171/2171]\n", "\n", "Removing ./index.html?C=S;O=D.tmp since it should be rejected.\n", "\n", "--2021-05-17 20:52:14-- https://gannet.fish.washington.edu/spartina/project-oyster-oa/Haws/bismark-2/multiqc_data/?C=D;O=D\n", "Reusing existing connection to gannet.fish.washington.edu:443.\n", "HTTP request sent, awaiting response... 200 OK\n", "Length: 2171 (2.1K) [text/html]\n", "Saving to: ‘./index.html?C=D;O=D.tmp’\n", "\n", "index.html?C=D;O=D. 100%[===================>] 2.12K --.-KB/s in 0s \n", "\n", "2021-05-17 20:52:14 (2.02 GB/s) - ‘./index.html?C=D;O=D.tmp’ saved [2171/2171]\n", "\n", "Removing ./index.html?C=D;O=D.tmp since it should be rejected.\n", "\n", "FINISHED --2021-05-17 20:52:14--\n", "Total wall clock time: 2m 7s\n", "Downloaded: 68 files, 5.6G in 1m 17s (74.0 MB/s)\n" ] } ], "source": [ "#Download 5x bedgraphs\n", "!wget -r \\\n", "--no-check-certificate --no-directories --no-parent --reject \"index.html*\" \\\n", "-P . \\\n", "-A \"*5x.bedgraph\" https://gannet.fish.washington.edu/spartina/project-oyster-oa/Haws/bismark-2/" ] }, { "cell_type": "code", "execution_count": 7, "metadata": { "collapsed": false, "scrolled": true }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "total 11482968\r\n", "-rw-r--r-- 1 yaamini staff 240M Mar 11 02:25 zr3644_10_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph\r\n", "-rw-r--r-- 1 yaamini staff 251M Mar 11 02:25 zr3644_11_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph\r\n", "-rw-r--r-- 1 yaamini staff 227M Mar 11 02:25 zr3644_12_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph\r\n", "-rw-r--r-- 1 yaamini staff 247M Mar 11 02:26 zr3644_13_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph\r\n", "-rw-r--r-- 1 yaamini staff 191M Mar 11 02:26 zr3644_14_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph\r\n", "-rw-r--r-- 1 yaamini staff 258M Mar 11 02:26 zr3644_15_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph\r\n", "-rw-r--r-- 1 yaamini staff 227M Mar 11 02:26 zr3644_16_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph\r\n", "-rw-r--r-- 1 yaamini staff 244M Mar 11 02:27 zr3644_17_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph\r\n", "-rw-r--r-- 1 yaamini staff 235M Mar 11 02:27 zr3644_18_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph\r\n", "-rw-r--r-- 1 yaamini staff 232M Mar 11 02:27 zr3644_19_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph\r\n", "-rw-r--r-- 1 yaamini staff 227M Mar 11 02:27 zr3644_1_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph\r\n", "-rw-r--r-- 1 yaamini staff 244M Mar 11 02:28 zr3644_20_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph\r\n", "-rw-r--r-- 1 yaamini staff 240M Mar 11 02:28 zr3644_21_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph\r\n", "-rw-r--r-- 1 yaamini staff 225M Mar 11 02:28 zr3644_22_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph\r\n", "-rw-r--r-- 1 yaamini staff 201M Mar 11 02:28 zr3644_23_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph\r\n", "-rw-r--r-- 1 yaamini staff 239M Mar 11 02:29 zr3644_24_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph\r\n", "-rw-r--r-- 1 yaamini staff 247M Mar 11 02:29 zr3644_2_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph\r\n", "-rw-r--r-- 1 yaamini staff 203M Mar 11 02:29 zr3644_3_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph\r\n", "-rw-r--r-- 1 yaamini staff 235M Mar 11 02:29 zr3644_4_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph\r\n", "-rw-r--r-- 1 yaamini staff 221M Mar 11 02:30 zr3644_5_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph\r\n", "-rw-r--r-- 1 yaamini staff 243M Mar 11 02:30 zr3644_6_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph\r\n", "-rw-r--r-- 1 yaamini staff 298M Mar 11 02:30 zr3644_7_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph\r\n", "-rw-r--r-- 1 yaamini staff 213M Mar 11 02:31 zr3644_8_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph\r\n", "-rw-r--r-- 1 yaamini staff 218M Mar 11 02:31 zr3644_9_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph\r\n" ] } ], "source": [ "#Check directory for all files\n", "!ls -lh" ] }, { "cell_type": "code", "execution_count": 8, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "MD5 (zr3644_10_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph) = f0dc26c38229b3640fa93fb29e1fa491\n", "MD5 (zr3644_11_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph) = 0fd1e7003a0cb80de0e094cfdb8a7d0a\n", "MD5 (zr3644_12_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph) = f4c8c3b70c40770c6d3376a2b7140925\n", "MD5 (zr3644_13_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph) = 54cc1f3a915e03c34aa905fff5be2b63\n", "MD5 (zr3644_14_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph) = cba3c994a0dc7502a64c5e0ae2c8727d\n", "MD5 (zr3644_15_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph) = 9d54e2bd92b198b7ba4ab036d297b801\n", "MD5 (zr3644_16_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph) = 54a28e3fd4ce60f6908ff11fc84e72c2\n", "MD5 (zr3644_17_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph) = 650e074555739b4aac40df54abc79814\n", "MD5 (zr3644_18_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph) = 2736303b8d17bce072892b08ac1ad978\n", "MD5 (zr3644_19_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph) = 28ec1746f1cd1122eaea62bec434d38d\n", "MD5 (zr3644_1_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph) = 2503628f1878ccbd7896e344d7b59b7e\n", "MD5 (zr3644_20_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph) = 8fb3cddf5456db9fa34f811160ed43d4\n", "MD5 (zr3644_21_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph) = 715237cee96784068c8e8235751ebd59\n", "MD5 (zr3644_22_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph) = c1afbf70c7246c2f024b839917df82fb\n", "MD5 (zr3644_23_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph) = c86bcefa56dc2bdde66882c090c72d7b\n", "MD5 (zr3644_24_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph) = ff86f7c813db1977bbfd498b47b39aa8\n", "MD5 (zr3644_2_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph) = 2f3f9b9a55a112f70a7c77ec58f58792\n", "MD5 (zr3644_3_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph) = 9e0ec9815033382dd7e0bbb19881568c\n", "MD5 (zr3644_4_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph) = a5d35602cd7072a3c126dc966c4016fb\n", "MD5 (zr3644_5_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph) = b2262d9ebd98790380fe724ee2c02edf\n", "MD5 (zr3644_6_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph) = a292bfa5e869aa2bb0ead3ba26d94e31\n", "MD5 (zr3644_7_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph) = 304a82d417d018107f4361f57a8eb047\n", "MD5 (zr3644_8_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph) = 9e4ba208aa2b28af19f34c089c8c8b36\n", "MD5 (zr3644_9_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph) = 0e9c8026b61cc46e0726bd3d977a5de0\n" ] } ], "source": [ "#Obtain md5\n", "!md5 *" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "## 2. Concatenate 1x methylation information" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "I will use `unionBedGraphs` to concatenate information for all loci across samples." ] }, { "cell_type": "code", "execution_count": 4, "metadata": { "collapsed": true }, "outputs": [], "source": [ "bedtoolsDirectory = \"/Users/Shared/bioinformatics/bedtools2/bin/\"" ] }, { "cell_type": "code", "execution_count": 10, "metadata": { "collapsed": false, "scrolled": true }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "\r\n", "Tool: bedtools unionbedg (aka unionBedGraphs)\r\n", "Version: v2.26.0\r\n", "Summary: Combines multiple BedGraph files into a single file,\r\n", "\t allowing coverage comparisons between them.\r\n", "\r\n", "Usage: bedtools unionbedg [OPTIONS] -i FILE1 FILE2 .. FILEn\r\n", "\t Assumes that each BedGraph file is sorted by chrom/start \r\n", "\t and that the intervals in each are non-overlapping.\r\n", "\r\n", "Options: \r\n", "\t-header\t\tPrint a header line.\r\n", "\t\t\t(chrom/start/end + names of each file).\r\n", "\r\n", "\t-names\t\tA list of names (one/file) to describe each file in -i.\r\n", "\t\t\tThese names will be printed in the header line.\r\n", "\r\n", "\t-g\t\tUse genome file to calculate empty regions.\r\n", "\t\t\t- STRING.\r\n", "\r\n", "\t-empty\t\tReport empty regions (i.e., start/end intervals w/o\r\n", "\t\t\tvalues in all files).\r\n", "\t\t\t- Requires the '-g FILE' parameter.\r\n", "\r\n", "\t-filler TEXT\tUse TEXT when representing intervals having no value.\r\n", "\t\t\t- Default is '0', but you can use 'N/A' or any text.\r\n", "\r\n", "\t-examples\tShow detailed usage examples.\r\n", "\r\n" ] } ], "source": [ "!{bedtoolsDirectory}unionBedGraphs -h" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "### 2a. Create a union BEDgraph" ] }, { "cell_type": "code", "execution_count": 17, "metadata": { "collapsed": true }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "building file list ... \n", "24 files to consider\n", "zr3644_10_R1_val_1_val_1_val_1_bismark_bt2_pe..CpG_report.merged_CpG_evidence.cov\n", " 443999580 100% 48.14MB/s 0:00:08 (xfer#1, to-check=23/24)\n", "zr3644_11_R1_val_1_val_1_val_1_bismark_bt2_pe..CpG_report.merged_CpG_evidence.cov\n", " 449661867 100% 45.31MB/s 0:00:09 (xfer#2, to-check=22/24)\n", "zr3644_12_R1_val_1_val_1_val_1_bismark_bt2_pe..CpG_report.merged_CpG_evidence.cov\n", " 439244022 100% 46.69MB/s 0:00:08 (xfer#3, to-check=21/24)\n", "zr3644_13_R1_val_1_val_1_val_1_bismark_bt2_pe..CpG_report.merged_CpG_evidence.cov\n", " 447737467 100% 44.12MB/s 0:00:09 (xfer#4, to-check=20/24)\n", "zr3644_14_R1_val_1_val_1_val_1_bismark_bt2_pe..CpG_report.merged_CpG_evidence.cov\n", " 410215416 100% 43.46MB/s 0:00:09 (xfer#5, to-check=19/24)\n", "zr3644_15_R1_val_1_val_1_val_1_bismark_bt2_pe..CpG_report.merged_CpG_evidence.cov\n", " 451618171 100% 44.59MB/s 0:00:09 (xfer#6, to-check=18/24)\n", "zr3644_16_R1_val_1_val_1_val_1_bismark_bt2_pe..CpG_report.merged_CpG_evidence.cov\n", " 436757128 100% 45.79MB/s 0:00:09 (xfer#7, to-check=17/24)\n", "zr3644_17_R1_val_1_val_1_val_1_bismark_bt2_pe..CpG_report.merged_CpG_evidence.cov\n", " 434181566 100% 46.89MB/s 0:00:08 (xfer#8, to-check=16/24)\n", "zr3644_18_R1_val_1_val_1_val_1_bismark_bt2_pe..CpG_report.merged_CpG_evidence.cov\n", " 441807091 100% 44.97MB/s 0:00:09 (xfer#9, to-check=15/24)\n", "zr3644_19_R1_val_1_val_1_val_1_bismark_bt2_pe..CpG_report.merged_CpG_evidence.cov\n", " 442130872 100% 47.06MB/s 0:00:08 (xfer#10, to-check=14/24)\n", "zr3644_1_R1_val_1_val_1_val_1_bismark_bt2_pe..CpG_report.merged_CpG_evidence.cov\n", " 424135061 100% 44.24MB/s 0:00:09 (xfer#11, to-check=13/24)\n", "zr3644_20_R1_val_1_val_1_val_1_bismark_bt2_pe..CpG_report.merged_CpG_evidence.cov\n", " 447382883 100% 47.79MB/s 0:00:08 (xfer#12, to-check=12/24)\n", "zr3644_21_R1_val_1_val_1_val_1_bismark_bt2_pe..CpG_report.merged_CpG_evidence.cov\n", " 445117118 100% 44.52MB/s 0:00:09 (xfer#13, to-check=11/24)\n", "zr3644_22_R1_val_1_val_1_val_1_bismark_bt2_pe..CpG_report.merged_CpG_evidence.cov\n", " 436556632 100% 46.20MB/s 0:00:09 (xfer#14, to-check=10/24)\n", "zr3644_23_R1_val_1_val_1_val_1_bismark_bt2_pe..CpG_report.merged_CpG_evidence.cov\n", " 427636223 100% 45.55MB/s 0:00:08 (xfer#15, to-check=9/24)\n", "zr3644_24_R1_val_1_val_1_val_1_bismark_bt2_pe..CpG_report.merged_CpG_evidence.cov\n", " 442700790 100% 44.31MB/s 0:00:09 (xfer#16, to-check=8/24)\n", "zr3644_2_R1_val_1_val_1_val_1_bismark_bt2_pe..CpG_report.merged_CpG_evidence.cov\n", " 436094286 100% 44.73MB/s 0:00:09 (xfer#17, to-check=7/24)\n", "zr3644_3_R1_val_1_val_1_val_1_bismark_bt2_pe..CpG_report.merged_CpG_evidence.cov\n", " 432708920 100% 48.23MB/s 0:00:08 (xfer#18, to-check=6/24)\n", "zr3644_4_R1_val_1_val_1_val_1_bismark_bt2_pe..CpG_report.merged_CpG_evidence.cov\n", " 444562817 100% 44.07MB/s 0:00:09 (xfer#19, to-check=5/24)\n", "zr3644_5_R1_val_1_val_1_val_1_bismark_bt2_pe..CpG_report.merged_CpG_evidence.cov\n", " 436724546 100% 45.71MB/s 0:00:09 (xfer#20, to-check=4/24)\n", "zr3644_6_R1_val_1_val_1_val_1_bismark_bt2_pe..CpG_report.merged_CpG_evidence.cov\n", " 445362200 100% 46.70MB/s 0:00:09 (xfer#21, to-check=3/24)\n", "zr3644_7_R1_val_1_val_1_val_1_bismark_bt2_pe..CpG_report.merged_CpG_evidence.cov\n", " 470209215 100% 45.57MB/s 0:00:09 (xfer#22, to-check=2/24)\n", "zr3644_8_R1_val_1_val_1_val_1_bismark_bt2_pe..CpG_report.merged_CpG_evidence.cov\n", " 433334314 100% 44.71MB/s 0:00:09 (xfer#23, to-check=1/24)\n", "zr3644_9_R1_val_1_val_1_val_1_bismark_bt2_pe..CpG_report.merged_CpG_evidence.cov\n", " 434307274 100% 48.02MB/s 0:00:08 (xfer#24, to-check=0/24)\n", "\n", "sent 10555476948 bytes received 548 bytes 50625791.35 bytes/sec\n", "total size is 10554185459 speedup is 1.00\n" ] } ], "source": [ "!rsync --archive --progress --verbose /Volumes/web/spartina/project-oyster-oa/Haws/bismark-2/*cov ." ] }, { "cell_type": "code", "execution_count": 18, "metadata": { "collapsed": false, "scrolled": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "zr3644_10_R1_val_1_val_1_val_1_bismark_bt2_pe..CpG_report.merged_CpG_evidence.cov\r\n", "zr3644_11_R1_val_1_val_1_val_1_bismark_bt2_pe..CpG_report.merged_CpG_evidence.cov\r\n", "zr3644_12_R1_val_1_val_1_val_1_bismark_bt2_pe..CpG_report.merged_CpG_evidence.cov\r\n", "zr3644_13_R1_val_1_val_1_val_1_bismark_bt2_pe..CpG_report.merged_CpG_evidence.cov\r\n", "zr3644_14_R1_val_1_val_1_val_1_bismark_bt2_pe..CpG_report.merged_CpG_evidence.cov\r\n", "zr3644_15_R1_val_1_val_1_val_1_bismark_bt2_pe..CpG_report.merged_CpG_evidence.cov\r\n", "zr3644_16_R1_val_1_val_1_val_1_bismark_bt2_pe..CpG_report.merged_CpG_evidence.cov\r\n", "zr3644_17_R1_val_1_val_1_val_1_bismark_bt2_pe..CpG_report.merged_CpG_evidence.cov\r\n", "zr3644_18_R1_val_1_val_1_val_1_bismark_bt2_pe..CpG_report.merged_CpG_evidence.cov\r\n", "zr3644_19_R1_val_1_val_1_val_1_bismark_bt2_pe..CpG_report.merged_CpG_evidence.cov\r\n", "zr3644_1_R1_val_1_val_1_val_1_bismark_bt2_pe..CpG_report.merged_CpG_evidence.cov\r\n", "zr3644_20_R1_val_1_val_1_val_1_bismark_bt2_pe..CpG_report.merged_CpG_evidence.cov\r\n", "zr3644_21_R1_val_1_val_1_val_1_bismark_bt2_pe..CpG_report.merged_CpG_evidence.cov\r\n", "zr3644_22_R1_val_1_val_1_val_1_bismark_bt2_pe..CpG_report.merged_CpG_evidence.cov\r\n", "zr3644_23_R1_val_1_val_1_val_1_bismark_bt2_pe..CpG_report.merged_CpG_evidence.cov\r\n", "zr3644_24_R1_val_1_val_1_val_1_bismark_bt2_pe..CpG_report.merged_CpG_evidence.cov\r\n", "zr3644_2_R1_val_1_val_1_val_1_bismark_bt2_pe..CpG_report.merged_CpG_evidence.cov\r\n", "zr3644_3_R1_val_1_val_1_val_1_bismark_bt2_pe..CpG_report.merged_CpG_evidence.cov\r\n", "zr3644_4_R1_val_1_val_1_val_1_bismark_bt2_pe..CpG_report.merged_CpG_evidence.cov\r\n", "zr3644_5_R1_val_1_val_1_val_1_bismark_bt2_pe..CpG_report.merged_CpG_evidence.cov\r\n", "zr3644_6_R1_val_1_val_1_val_1_bismark_bt2_pe..CpG_report.merged_CpG_evidence.cov\r\n", "zr3644_7_R1_val_1_val_1_val_1_bismark_bt2_pe..CpG_report.merged_CpG_evidence.cov\r\n", "zr3644_8_R1_val_1_val_1_val_1_bismark_bt2_pe..CpG_report.merged_CpG_evidence.cov\r\n", "zr3644_9_R1_val_1_val_1_val_1_bismark_bt2_pe..CpG_report.merged_CpG_evidence.cov\r\n" ] } ], "source": [ "!find *cov" ] }, { "cell_type": "code", "execution_count": 33, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "NC_001276.1\t34\t36\t5.303030\t7\t125\r\n", "NC_001276.1\t123\t125\t1.315789\t5\t375\r\n", "NC_001276.1\t305\t307\t3.873239\t11\t273\r\n", "NC_001276.1\t433\t435\t2.153110\t9\t409\r\n", "NC_001276.1\t457\t459\t1.830664\t8\t429\r\n", "NC_001276.1\t482\t484\t0.477327\t2\t417\r\n", "NC_001276.1\t609\t611\t1.716738\t8\t458\r\n", "NC_001276.1\t781\t783\t1.434426\t7\t481\r\n", "NC_001276.1\t826\t828\t1.162791\t5\t425\r\n", "NC_001276.1\t951\t953\t3.603604\t12\t321\r\n" ] } ], "source": [ "#Columns: chr, start, end, %meth, reads meth, reads unmeth\n", "!head zr3644_9_R1_val_1_val_1_val_1_bismark_bt2_pe..CpG_report.merged_CpG_evidence.cov" ] }, { "cell_type": "code", "execution_count": 34, "metadata": { "collapsed": true }, "outputs": [], "source": [ "%%bash\n", "\n", "for f in *.cov\n", "do\n", " awk '{print $1\"\\t\"$2\"\\t\"$3\"\\t\"$4}' ${f} \\\n", " > $(basename ${f%..CpG_report.merged_CpG_evidence.cov})_1x.bedgraph\n", "done" ] }, { "cell_type": "code", "execution_count": 38, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "zr3644_10_R1_val_1_val_1_val_1_bismark_bt2_pe_1x.bedgraph\r\n", "zr3644_11_R1_val_1_val_1_val_1_bismark_bt2_pe_1x.bedgraph\r\n", "zr3644_12_R1_val_1_val_1_val_1_bismark_bt2_pe_1x.bedgraph\r\n", "zr3644_13_R1_val_1_val_1_val_1_bismark_bt2_pe_1x.bedgraph\r\n", "zr3644_14_R1_val_1_val_1_val_1_bismark_bt2_pe_1x.bedgraph\r\n", "zr3644_15_R1_val_1_val_1_val_1_bismark_bt2_pe_1x.bedgraph\r\n", "zr3644_16_R1_val_1_val_1_val_1_bismark_bt2_pe_1x.bedgraph\r\n", "zr3644_17_R1_val_1_val_1_val_1_bismark_bt2_pe_1x.bedgraph\r\n", "zr3644_18_R1_val_1_val_1_val_1_bismark_bt2_pe_1x.bedgraph\r\n", "zr3644_19_R1_val_1_val_1_val_1_bismark_bt2_pe_1x.bedgraph\r\n", "zr3644_1_R1_val_1_val_1_val_1_bismark_bt2_pe_1x.bedgraph\r\n", "zr3644_20_R1_val_1_val_1_val_1_bismark_bt2_pe_1x.bedgraph\r\n", "zr3644_21_R1_val_1_val_1_val_1_bismark_bt2_pe_1x.bedgraph\r\n", "zr3644_22_R1_val_1_val_1_val_1_bismark_bt2_pe_1x.bedgraph\r\n", "zr3644_23_R1_val_1_val_1_val_1_bismark_bt2_pe_1x.bedgraph\r\n", "zr3644_24_R1_val_1_val_1_val_1_bismark_bt2_pe_1x.bedgraph\r\n", "zr3644_2_R1_val_1_val_1_val_1_bismark_bt2_pe_1x.bedgraph\r\n", "zr3644_3_R1_val_1_val_1_val_1_bismark_bt2_pe_1x.bedgraph\r\n", "zr3644_4_R1_val_1_val_1_val_1_bismark_bt2_pe_1x.bedgraph\r\n", "zr3644_5_R1_val_1_val_1_val_1_bismark_bt2_pe_1x.bedgraph\r\n", "zr3644_6_R1_val_1_val_1_val_1_bismark_bt2_pe_1x.bedgraph\r\n", "zr3644_7_R1_val_1_val_1_val_1_bismark_bt2_pe_1x.bedgraph\r\n", "zr3644_8_R1_val_1_val_1_val_1_bismark_bt2_pe_1x.bedgraph\r\n", "zr3644_9_R1_val_1_val_1_val_1_bismark_bt2_pe_1x.bedgraph\r\n" ] } ], "source": [ "!find *1x.bedgraph" ] }, { "cell_type": "code", "execution_count": 39, "metadata": { "collapsed": true }, "outputs": [], "source": [ "%%bash\n", "\n", "for f in *1x.bedgraph\n", "do\n", " /Users/Shared/bioinformatics/bedtools2/bin/sortBed \\\n", " -i ${f} \\\n", " > $(basename ${f%_1x.bedgraph})_1x.sort.bedgraph\n", "done" ] }, { "cell_type": "code", "execution_count": 40, "metadata": { "collapsed": false, "scrolled": true }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "zr3644_10_R1_val_1_val_1_val_1_bismark_bt2_pe_1x.sort.bedgraph\r\n", "zr3644_11_R1_val_1_val_1_val_1_bismark_bt2_pe_1x.sort.bedgraph\r\n", "zr3644_12_R1_val_1_val_1_val_1_bismark_bt2_pe_1x.sort.bedgraph\r\n", "zr3644_13_R1_val_1_val_1_val_1_bismark_bt2_pe_1x.sort.bedgraph\r\n", "zr3644_14_R1_val_1_val_1_val_1_bismark_bt2_pe_1x.sort.bedgraph\r\n", "zr3644_15_R1_val_1_val_1_val_1_bismark_bt2_pe_1x.sort.bedgraph\r\n", "zr3644_16_R1_val_1_val_1_val_1_bismark_bt2_pe_1x.sort.bedgraph\r\n", "zr3644_17_R1_val_1_val_1_val_1_bismark_bt2_pe_1x.sort.bedgraph\r\n", "zr3644_18_R1_val_1_val_1_val_1_bismark_bt2_pe_1x.sort.bedgraph\r\n", "zr3644_19_R1_val_1_val_1_val_1_bismark_bt2_pe_1x.sort.bedgraph\r\n", "zr3644_1_R1_val_1_val_1_val_1_bismark_bt2_pe_1x.sort.bedgraph\r\n", "zr3644_20_R1_val_1_val_1_val_1_bismark_bt2_pe_1x.sort.bedgraph\r\n", "zr3644_21_R1_val_1_val_1_val_1_bismark_bt2_pe_1x.sort.bedgraph\r\n", "zr3644_22_R1_val_1_val_1_val_1_bismark_bt2_pe_1x.sort.bedgraph\r\n", "zr3644_23_R1_val_1_val_1_val_1_bismark_bt2_pe_1x.sort.bedgraph\r\n", "zr3644_24_R1_val_1_val_1_val_1_bismark_bt2_pe_1x.sort.bedgraph\r\n", "zr3644_2_R1_val_1_val_1_val_1_bismark_bt2_pe_1x.sort.bedgraph\r\n", "zr3644_3_R1_val_1_val_1_val_1_bismark_bt2_pe_1x.sort.bedgraph\r\n", "zr3644_4_R1_val_1_val_1_val_1_bismark_bt2_pe_1x.sort.bedgraph\r\n", "zr3644_5_R1_val_1_val_1_val_1_bismark_bt2_pe_1x.sort.bedgraph\r\n", "zr3644_6_R1_val_1_val_1_val_1_bismark_bt2_pe_1x.sort.bedgraph\r\n", "zr3644_7_R1_val_1_val_1_val_1_bismark_bt2_pe_1x.sort.bedgraph\r\n", "zr3644_8_R1_val_1_val_1_val_1_bismark_bt2_pe_1x.sort.bedgraph\r\n", "zr3644_9_R1_val_1_val_1_val_1_bismark_bt2_pe_1x.sort.bedgraph\r\n" ] } ], "source": [ "!ls *1x.sort.bedgraph" ] }, { "cell_type": "code", "execution_count": 41, "metadata": { "collapsed": false }, "outputs": [], "source": [ "#Create union BEDgraph from sorted files\n", "#Include a header\n", "#Use N/A when there is no data for a CpG in a sample\n", "#Define sample IDs\n", "#Use sorted bedgraphs\n", "#Save output\n", "!{bedtoolsDirectory}unionBedGraphs \\\n", "-header \\\n", "-filler N/A \\\n", "-names 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 \\\n", "-i \\\n", "*1x.sort.bedgraph \\\n", "> union_1x.bedgraph" ] }, { "cell_type": "code", "execution_count": 42, "metadata": { "collapsed": false, "scrolled": true }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "chrom\tstart\tend\t1\t2\t3\t4\t5\t6\t7\t8\t9\t10\t11\t12\t13\t14\t15\t16\t17\t18\t19\t20\t21\t22\t23\t24\n", "NC_001276.1\t34\t36\t3.092784\t1.162791\t3.061224\t3.401361\t3.614458\t2.659574\t4.375000\t4.347826\t4.054054\t3.603604\t2.343750\t3.468208\t2.083333\t2.453988\t6.250000\t5.479452\t9.615385\t6.862745\t5.217391\t1.785714\t2.150538\t3.389831\t2.380952\t5.303030\n", "NC_001276.1\t123\t125\t0.851064\t0.425532\t0.826446\t0.755668\t1.562500\t0.821355\t0.493827\t1.100917\t0.819672\t0.387597\t2.006689\t0.956938\t0.000000\t0.512821\t1.115242\t1.020408\t0.378788\t0.396825\t1.689189\t0.727273\t1.176471\t0.845666\t1.287554\t1.315789\n", "NC_001276.1\t305\t307\t3.314917\t1.081081\t3.225806\t1.955307\t6.578947\t2.739726\t1.973684\t2.403846\t2.427184\t1.777778\t2.525253\t3.669725\t4.848485\t3.846154\t3.255814\t5.166052\t2.843602\t5.687204\t2.517986\t1.621622\t1.630435\t4.450262\t4.040404\t3.873239\n", "NC_001276.1\t433\t435\t1.986755\t1.167315\t1.133144\t0.569260\t0.881057\t1.798561\t1.212121\t1.658375\t1.292407\t1.273885\t0.284900\t1.541426\t0.743494\t0.649351\t1.562500\t1.834862\t1.277955\t2.473498\t0.997506\t1.506024\t1.683502\t1.680672\t2.135231\t2.153110\n", "NC_001276.1\t457\t459\t1.538462\t2.158273\t0.529101\t0.172117\t1.195219\t1.487603\t0.560748\t1.397516\t0.765697\t1.479290\t1.033592\t0.910747\t1.754386\t0.769231\t0.857143\t0.643777\t1.159420\t0.619195\t2.142857\t1.983003\t1.238390\t1.374046\t2.317881\t1.830664\n", "NC_001276.1\t482\t484\t0.638978\t2.076125\t1.749271\t0.743494\t0.000000\t1.587302\t1.242236\t1.490066\t1.162791\t1.428571\t1.149425\t0.589391\t0.729927\t1.568627\t1.269841\t1.207729\t2.395210\t1.612903\t1.790281\t1.436782\t0.911854\t1.176471\t1.736111\t0.477327\n", "NC_001276.1\t609\t611\t1.479290\t1.543210\t2.425876\t1.589825\t1.742160\t1.497006\t1.876173\t1.923077\t2.737752\t1.734104\t0.997506\t2.101576\t2.654867\t1.883562\t2.777778\t2.024291\t1.837270\t3.954802\t0.938967\t3.359173\t3.200000\t2.352941\t2.866242\t1.716738\n", "NC_001276.1\t781\t783\t1.457726\t1.298701\t1.941748\t1.379310\t2.238806\t1.121795\t1.740812\t3.153153\t2.489019\t2.747253\t2.843602\t1.325758\t1.597444\t1.449275\t3.651685\t1.840491\t1.608579\t2.295082\t1.909308\t2.209945\t2.727273\t3.744150\t3.508772\t1.434426\n", "NC_001276.1\t826\t828\t1.346801\t2.205882\t2.298851\t0.200401\t0.823045\t2.161100\t0.883002\t2.117264\t1.036269\t1.796407\t0.831025\t1.237113\t1.379310\t1.131222\t1.010101\t1.345291\t1.333333\t1.503759\t0.879765\t1.577287\t1.048951\t2.229846\t1.886792\t1.162791\n", " 12794075 union_1x.bedgraph\n" ] } ], "source": [ "#Check output\n", "!head union_1x.bedgraph\n", "!wc -l union_1x.bedgraph" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "## 3. Concatenate 5x methylation information" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "### 3a. Create a union BEDgraph" ] }, { "cell_type": "code", "execution_count": 11, "metadata": { "collapsed": true }, "outputs": [], "source": [ "%%bash\n", "\n", "for f in *5x.bedgraph\n", "do\n", "/Users/Shared/bioinformatics/bedtools2/bin/sortBed \\\n", "-i ${f} \\\n", "> $(basename ${f%_5x.bedgraph})_5x.sort.bedgraph\n", "done" ] }, { "cell_type": "code", "execution_count": 12, "metadata": { "collapsed": false, "scrolled": true }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "zr3644_10_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.sort.bedgraph\r\n", "zr3644_11_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.sort.bedgraph\r\n", "zr3644_12_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.sort.bedgraph\r\n", "zr3644_13_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.sort.bedgraph\r\n", "zr3644_14_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.sort.bedgraph\r\n", "zr3644_15_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.sort.bedgraph\r\n", "zr3644_16_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.sort.bedgraph\r\n", "zr3644_17_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.sort.bedgraph\r\n", "zr3644_18_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.sort.bedgraph\r\n", "zr3644_19_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.sort.bedgraph\r\n", "zr3644_1_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.sort.bedgraph\r\n", "zr3644_20_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.sort.bedgraph\r\n", "zr3644_21_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.sort.bedgraph\r\n", "zr3644_22_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.sort.bedgraph\r\n", "zr3644_23_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.sort.bedgraph\r\n", "zr3644_24_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.sort.bedgraph\r\n", "zr3644_2_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.sort.bedgraph\r\n", "zr3644_3_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.sort.bedgraph\r\n", "zr3644_4_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.sort.bedgraph\r\n", "zr3644_5_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.sort.bedgraph\r\n", "zr3644_6_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.sort.bedgraph\r\n", "zr3644_7_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.sort.bedgraph\r\n", "zr3644_8_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.sort.bedgraph\r\n", "zr3644_9_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.sort.bedgraph\r\n" ] } ], "source": [ "!ls *sort*" ] }, { "cell_type": "code", "execution_count": 13, "metadata": { "collapsed": false }, "outputs": [], "source": [ "#Create union BEDgraph from sorted files\n", "#Include a header\n", "#Use N/A when there is no data for a CpG in a sample\n", "#Define sample IDs\n", "#Use sorted bedgraphs\n", "#Save output\n", "!{bedtoolsDirectory}unionBedGraphs \\\n", "-header \\\n", "-filler N/A \\\n", "-names 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 \\\n", "-i \\\n", "*5x.sort.bedgraph \\\n", "> union_5x.bedgraph" ] }, { "cell_type": "code", "execution_count": 14, "metadata": { "collapsed": false, "scrolled": true }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "chrom\tstart\tend\t1\t2\t3\t4\t5\t6\t7\t8\t9\t10\t11\t12\t13\t14\t15\t16\t17\t18\t19\t20\t21\t22\t23\t24\n", "NC_001276.1\t34\t36\t3.092784\t1.162791\t3.061224\t3.401361\t3.614458\t2.659574\t4.375000\t4.347826\t4.054054\t3.603604\t2.343750\t3.468208\t2.083333\t2.453988\t6.250000\t5.479452\t9.615385\t6.862745\t5.217391\t1.785714\t2.150538\t3.389831\t2.380952\t5.303030\n", "NC_001276.1\t123\t125\t0.851064\t0.425532\t0.826446\t0.755668\t1.562500\t0.821355\t0.493827\t1.100917\t0.819672\t0.387597\t2.006689\t0.956938\t0.000000\t0.512821\t1.115242\t1.020408\t0.378788\t0.396825\t1.689189\t0.727273\t1.176471\t0.845666\t1.287554\t1.315789\n", "NC_001276.1\t305\t307\t3.314917\t1.081081\t3.225806\t1.955307\t6.578947\t2.739726\t1.973684\t2.403846\t2.427184\t1.777778\t2.525253\t3.669725\t4.848485\t3.846154\t3.255814\t5.166052\t2.843602\t5.687204\t2.517986\t1.621622\t1.630435\t4.450262\t4.040404\t3.873239\n", "NC_001276.1\t433\t435\t1.986755\t1.167315\t1.133144\t0.569260\t0.881057\t1.798561\t1.212121\t1.658375\t1.292407\t1.273885\t0.284900\t1.541426\t0.743494\t0.649351\t1.562500\t1.834862\t1.277955\t2.473498\t0.997506\t1.506024\t1.683502\t1.680672\t2.135231\t2.153110\n", "NC_001276.1\t457\t459\t1.538462\t2.158273\t0.529101\t0.172117\t1.195219\t1.487603\t0.560748\t1.397516\t0.765697\t1.479290\t1.033592\t0.910747\t1.754386\t0.769231\t0.857143\t0.643777\t1.159420\t0.619195\t2.142857\t1.983003\t1.238390\t1.374046\t2.317881\t1.830664\n", "NC_001276.1\t482\t484\t0.638978\t2.076125\t1.749271\t0.743494\t0.000000\t1.587302\t1.242236\t1.490066\t1.162791\t1.428571\t1.149425\t0.589391\t0.729927\t1.568627\t1.269841\t1.207729\t2.395210\t1.612903\t1.790281\t1.436782\t0.911854\t1.176471\t1.736111\t0.477327\n", "NC_001276.1\t609\t611\t1.479290\t1.543210\t2.425876\t1.589825\t1.742160\t1.497006\t1.876173\t1.923077\t2.737752\t1.734104\t0.997506\t2.101576\t2.654867\t1.883562\t2.777778\t2.024291\t1.837270\t3.954802\t0.938967\t3.359173\t3.200000\t2.352941\t2.866242\t1.716738\n", "NC_001276.1\t781\t783\t1.457726\t1.298701\t1.941748\t1.379310\t2.238806\t1.121795\t1.740812\t3.153153\t2.489019\t2.747253\t2.843602\t1.325758\t1.597444\t1.449275\t3.651685\t1.840491\t1.608579\t2.295082\t1.909308\t2.209945\t2.727273\t3.744150\t3.508772\t1.434426\n", "NC_001276.1\t826\t828\t1.346801\t2.205882\t2.298851\t0.200401\t0.823045\t2.161100\t0.883002\t2.117264\t1.036269\t1.796407\t0.831025\t1.237113\t1.379310\t1.131222\t1.010101\t1.345291\t1.333333\t1.503759\t0.879765\t1.577287\t1.048951\t2.229846\t1.886792\t1.162791\n", " 10497321 union_5x.bedgraph\n" ] } ], "source": [ "#Check output\n", "!head union_5x.bedgraph\n", "!wc -l union_5x.bedgraph" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "### 3b. Manipulate with `pandas`" ] }, { "cell_type": "code", "execution_count": 5, "metadata": { "collapsed": false }, "outputs": [ { "data": { "text/html": [ "
\n", "\n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", "
chromstartend1234567...15161718192021222324
0NC_001276.134363.0927841.1627913.0612243.4013613.6144582.6595744.375000...6.2500005.4794529.6153856.8627455.2173911.7857142.1505383.3898312.3809525.303030
1NC_001276.11231250.8510640.4255320.8264460.7556681.5625000.8213550.493827...1.1152421.0204080.3787880.3968251.6891890.7272731.1764710.8456661.2875541.315789
2NC_001276.13053073.3149171.0810813.2258061.9553076.5789472.7397261.973684...3.2558145.1660522.8436025.6872042.5179861.6216221.6304354.4502624.0404043.873239
3NC_001276.14334351.9867551.1673151.1331440.5692600.8810571.7985611.212121...1.5625001.8348621.2779552.4734980.9975061.5060241.6835021.6806722.1352312.153110
4NC_001276.14574591.5384622.1582730.5291010.1721171.1952191.4876030.560748...0.8571430.6437771.1594200.6191952.1428571.9830031.2383901.3740462.3178811.830664
\n", "

5 rows × 27 columns

\n", "
" ], "text/plain": [ " chrom start end 1 2 3 4 5 \\\n", "0 NC_001276.1 34 36 3.092784 1.162791 3.061224 3.401361 3.614458 \n", "1 NC_001276.1 123 125 0.851064 0.425532 0.826446 0.755668 1.562500 \n", "2 NC_001276.1 305 307 3.314917 1.081081 3.225806 1.955307 6.578947 \n", "3 NC_001276.1 433 435 1.986755 1.167315 1.133144 0.569260 0.881057 \n", "4 NC_001276.1 457 459 1.538462 2.158273 0.529101 0.172117 1.195219 \n", "\n", " 6 7 ... 15 16 17 18 \\\n", "0 2.659574 4.375000 ... 6.250000 5.479452 9.615385 6.862745 \n", "1 0.821355 0.493827 ... 1.115242 1.020408 0.378788 0.396825 \n", "2 2.739726 1.973684 ... 3.255814 5.166052 2.843602 5.687204 \n", "3 1.798561 1.212121 ... 1.562500 1.834862 1.277955 2.473498 \n", "4 1.487603 0.560748 ... 0.857143 0.643777 1.159420 0.619195 \n", "\n", " 19 20 21 22 23 24 \n", "0 5.217391 1.785714 2.150538 3.389831 2.380952 5.303030 \n", "1 1.689189 0.727273 1.176471 0.845666 1.287554 1.315789 \n", "2 2.517986 1.621622 1.630435 4.450262 4.040404 3.873239 \n", "3 0.997506 1.506024 1.683502 1.680672 2.135231 2.153110 \n", "4 2.142857 1.983003 1.238390 1.374046 2.317881 1.830664 \n", "\n", "[5 rows x 27 columns]" ] }, "execution_count": 5, "metadata": {}, "output_type": "execute_result" } ], "source": [ "#Import union data into pandas\n", "#Check head\n", "df = pd.read_table(\"union_5x.bedgraph\")\n", "df.head(5)" ] }, { "cell_type": "code", "execution_count": 6, "metadata": { "collapsed": false }, "outputs": [ { "data": { "text/html": [ "
\n", "\n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", "
chromstartend1234567...161718192021222324total
10497310NW_022994998.154647546490.00.09.0909090.00.00.00.0...0.00.00.00.00.00.00.00.00.00.378788
10497311NW_022994998.154770547720.00.00.0000000.00.00.00.0...0.00.00.00.00.00.00.00.0NaN0.000000
10497312NW_022994998.154834548360.00.00.000000NaN0.00.00.0...0.00.00.00.00.00.00.0NaNNaN0.000000
10497313NW_022994998.154843548450.0NaN0.000000NaN0.00.010.0...0.00.00.00.00.00.00.0NaNNaN0.954545
10497314NW_022994998.154860548620.0NaN0.000000NaN0.00.00.0...NaN0.00.00.00.00.00.0NaNNaN0.000000
10497315NW_022994998.154872548740.0NaN0.000000NaN0.00.00.0...NaN0.00.00.00.00.00.0NaNNaN0.000000
10497316NW_022994998.154934549360.0NaN0.000000NaNNaN0.0NaN...NaNNaNNaNNaNNaNNaN0.00.0NaN0.000000
10497317NW_022994998.15494954951NaNNaNNaNNaNNaN0.0NaN...NaNNaNNaNNaNNaNNaNNaN0.0NaN0.000000
10497318NW_022994998.15495354955NaNNaNNaNNaNNaN0.0NaN...NaNNaNNaNNaNNaNNaNNaN0.0NaN0.000000
10497319NW_022994998.15495854960NaNNaNNaNNaNNaN0.0NaN...NaNNaNNaNNaNNaNNaNNaN0.0NaN0.000000
\n", "

10 rows × 28 columns

\n", "
" ], "text/plain": [ " chrom start end 1 2 3 4 5 6 \\\n", "10497310 NW_022994998.1 54647 54649 0.0 0.0 9.090909 0.0 0.0 0.0 \n", "10497311 NW_022994998.1 54770 54772 0.0 0.0 0.000000 0.0 0.0 0.0 \n", "10497312 NW_022994998.1 54834 54836 0.0 0.0 0.000000 NaN 0.0 0.0 \n", "10497313 NW_022994998.1 54843 54845 0.0 NaN 0.000000 NaN 0.0 0.0 \n", "10497314 NW_022994998.1 54860 54862 0.0 NaN 0.000000 NaN 0.0 0.0 \n", "10497315 NW_022994998.1 54872 54874 0.0 NaN 0.000000 NaN 0.0 0.0 \n", "10497316 NW_022994998.1 54934 54936 0.0 NaN 0.000000 NaN NaN 0.0 \n", "10497317 NW_022994998.1 54949 54951 NaN NaN NaN NaN NaN 0.0 \n", "10497318 NW_022994998.1 54953 54955 NaN NaN NaN NaN NaN 0.0 \n", "10497319 NW_022994998.1 54958 54960 NaN NaN NaN NaN NaN 0.0 \n", "\n", " 7 ... 16 17 18 19 20 21 22 23 24 \\\n", "10497310 0.0 ... 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 \n", "10497311 0.0 ... 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 NaN \n", "10497312 0.0 ... 0.0 0.0 0.0 0.0 0.0 0.0 0.0 NaN NaN \n", "10497313 10.0 ... 0.0 0.0 0.0 0.0 0.0 0.0 0.0 NaN NaN \n", "10497314 0.0 ... NaN 0.0 0.0 0.0 0.0 0.0 0.0 NaN NaN \n", "10497315 0.0 ... NaN 0.0 0.0 0.0 0.0 0.0 0.0 NaN NaN \n", "10497316 NaN ... NaN NaN NaN NaN NaN NaN 0.0 0.0 NaN \n", "10497317 NaN ... NaN NaN NaN NaN NaN NaN NaN 0.0 NaN \n", "10497318 NaN ... NaN NaN NaN NaN NaN NaN NaN 0.0 NaN \n", "10497319 NaN ... NaN NaN NaN NaN NaN NaN NaN 0.0 NaN \n", "\n", " total \n", "10497310 0.378788 \n", "10497311 0.000000 \n", "10497312 0.000000 \n", "10497313 0.954545 \n", "10497314 0.000000 \n", "10497315 0.000000 \n", "10497316 0.000000 \n", "10497317 0.000000 \n", "10497318 0.000000 \n", "10497319 0.000000 \n", "\n", "[10 rows x 28 columns]" ] }, "execution_count": 6, "metadata": {}, "output_type": "execute_result" } ], "source": [ "#Average all samples for total genome methylation information and save as a new column\n", "#NA are not included in averages\n", "#Check output\n", "df['total'] = df[['1', '2', '3', '4', '5', '6', '7', '8', '9', '10', '11', '12', '13', '14', '15', '16', '17', '18', '19', '20', '21', '22', '23', '24']].mean(axis=1)\n", "df.tail(10)" ] }, { "cell_type": "code", "execution_count": 17, "metadata": { "collapsed": true }, "outputs": [], "source": [ "#Save dataframe in a tabular format and include N/As. Do not include quotes.\n", "df.to_csv(\"union-averages.bedgraph\", sep = \"\\t\", na_rep = \"N/A\", quoting = 3)" ] }, { "cell_type": "code", "execution_count": 18, "metadata": { "collapsed": false, "scrolled": true }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "\tchrom\tstart\tend\t1\t2\t3\t4\t5\t6\t7\t8\t9\t10\t11\t12\t13\t14\t15\t16\t17\t18\t19\t20\t21\t22\t23\t24\ttotal\r\n", "0\tNC_001276.1\t34\t36\t3.092784\t1.162791\t3.061224\t3.401361\t3.6144580000000004\t2.659574\t4.375\t4.347826\t4.054054\t3.6036040000000003\t2.34375\t3.468208\t2.083333\t2.4539880000000003\t6.25\t5.479451999999999\t9.615385\t6.862744999999999\t5.217391\t1.785714\t2.150538\t3.3898309999999996\t2.380952\t5.303030000000001\t3.8398747083333338\r\n", "1\tNC_001276.1\t123\t125\t0.8510639999999999\t0.42553199999999997\t0.8264459999999999\t0.755668\t1.5625\t0.821355\t0.493827\t1.100917\t0.819672\t0.38759699999999997\t2.0066889999999997\t0.956938\t0.0\t0.512821\t1.115242\t1.020408\t0.378788\t0.396825\t1.689189\t0.727273\t1.1764709999999998\t0.845666\t1.287554\t1.3157889999999999\t0.894759625\r\n", "2\tNC_001276.1\t305\t307\t3.314917\t1.081081\t3.225806\t1.955307\t6.578947\t2.7397259999999997\t1.973684\t2.4038459999999997\t2.427184\t1.7777779999999999\t2.5252529999999997\t3.669725\t4.848485\t3.8461540000000003\t3.255814\t5.166052\t2.843602\t5.687204\t2.517986\t1.621622\t1.630435\t4.450262\t4.040404\t3.873239\t3.2272713749999995\r\n", "3\tNC_001276.1\t433\t435\t1.9867549999999998\t1.1673149999999999\t1.1331440000000002\t0.56926\t0.881057\t1.798561\t1.212121\t1.658375\t1.2924069999999999\t1.273885\t0.2849\t1.541426\t0.743494\t0.649351\t1.5625\t1.834862\t1.277955\t2.4734979999999998\t0.997506\t1.506024\t1.683502\t1.6806720000000002\t2.135231\t2.15311\t1.3957046250000003\r\n", "4\tNC_001276.1\t457\t459\t1.538462\t2.158273\t0.529101\t0.17211700000000002\t1.195219\t1.487603\t0.5607479999999999\t1.397516\t0.7656970000000001\t1.47929\t1.033592\t0.910747\t1.754386\t0.769231\t0.857143\t0.643777\t1.1594200000000001\t0.6191949999999999\t2.142857\t1.9830029999999998\t1.2383899999999999\t1.3740459999999999\t2.3178810000000003\t1.8306639999999998\t1.2465982500000001\r\n", "5\tNC_001276.1\t482\t484\t0.6389779999999999\t2.076125\t1.749271\t0.743494\t0.0\t1.587302\t1.2422360000000001\t1.490066\t1.162791\t1.4285709999999998\t1.149425\t0.589391\t0.729927\t1.568627\t1.269841\t1.207729\t2.39521\t1.612903\t1.7902810000000002\t1.436782\t0.911854\t1.1764709999999998\t1.736111\t0.47732700000000006\t1.2571130416666667\r\n", "6\tNC_001276.1\t609\t611\t1.47929\t1.54321\t2.4258759999999997\t1.589825\t1.74216\t1.497006\t1.8761729999999999\t1.9230770000000001\t2.737752\t1.734104\t0.997506\t2.1015759999999997\t2.654867\t1.883562\t2.777778\t2.024291\t1.8372700000000002\t3.9548019999999995\t0.938967\t3.359173\t3.2\t2.352941\t2.8662419999999997\t1.716738\t2.1339244166666664\r\n", "7\tNC_001276.1\t781\t783\t1.457726\t1.298701\t1.941748\t1.37931\t2.2388060000000003\t1.121795\t1.7408119999999998\t3.153153\t2.489019\t2.7472529999999997\t2.843602\t1.325758\t1.597444\t1.449275\t3.651685\t1.8404909999999999\t1.608579\t2.295082\t1.9093080000000002\t2.2099450000000003\t2.727273\t3.74415\t3.508772\t1.434426\t2.1547547083333334\r\n", "8\tNC_001276.1\t826\t828\t1.346801\t2.205882\t2.298851\t0.200401\t0.823045\t2.1611\t0.8830020000000001\t2.117264\t1.036269\t1.7964069999999999\t0.831025\t1.237113\t1.37931\t1.131222\t1.010101\t1.345291\t1.333333\t1.503759\t0.8797649999999999\t1.577287\t1.048951\t2.2298459999999998\t1.8867919999999998\t1.162791\t1.3927336666666665\r\n" ] } ], "source": [ "#Check pandas manipulations\n", "!head union-averages.bedgraph" ] }, { "cell_type": "code", "execution_count": 19, "metadata": { "collapsed": false }, "outputs": [], "source": [ "#Remove header\n", "#Keep chr, start, end, and the average\n", "#Save output\n", "! tail -n+2 union-averages.bedgraph \\\n", "| awk -F'\\t' -v OFS='\\t' '{print $2, $3, $4, $29}' \\\n", "> zr3644_union-averages_5x.bedgraph" ] }, { "cell_type": "code", "execution_count": 20, "metadata": { "collapsed": false, "scrolled": true }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "NC_001276.1\t34\t36\t3.8398747083333338\n", "NC_001276.1\t123\t125\t0.894759625\n", "NC_001276.1\t305\t307\t3.2272713749999995\n", "NC_001276.1\t433\t435\t1.3957046250000003\n", "NC_001276.1\t457\t459\t1.2465982500000001\n", "NC_001276.1\t482\t484\t1.2571130416666667\n", "NC_001276.1\t609\t611\t2.1339244166666664\n", "NC_001276.1\t781\t783\t2.1547547083333334\n", "NC_001276.1\t826\t828\t1.3927336666666665\n", "NC_001276.1\t951\t953\t3.3334975000000004\n", " 10497320 zr3644_union-averages_5x.bedgraph\n" ] } ], "source": [ "#Check output: chr, start, end, average %meth\n", "!head zr3644_union-averages_5x.bedgraph\n", "!wc -l zr3644_union-averages_5x.bedgraph" ] }, { "cell_type": "code", "execution_count": 7, "metadata": { "collapsed": false, "scrolled": true }, "outputs": [ { "data": { "text/html": [ "
\n", "\n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", "
chromstartend1234567...18192021222324totaldiploidtriploid
10497310NW_022994998.154647546490.00.09.0909090.00.00.00.0...0.00.00.00.00.00.00.00.3787880.7575760.0
10497311NW_022994998.154770547720.00.00.0000000.00.00.00.0...0.00.00.00.00.00.0NaN0.0000000.0000000.0
10497312NW_022994998.154834548360.00.00.000000NaN0.00.00.0...0.00.00.00.00.0NaNNaN0.0000000.0000000.0
10497313NW_022994998.154843548450.0NaN0.000000NaN0.00.010.0...0.00.00.00.00.0NaNNaN0.9545451.9090910.0
10497314NW_022994998.154860548620.0NaN0.000000NaN0.00.00.0...0.00.00.00.00.0NaNNaN0.0000000.0000000.0
10497315NW_022994998.154872548740.0NaN0.000000NaN0.00.00.0...0.00.00.00.00.0NaNNaN0.0000000.0000000.0
10497316NW_022994998.154934549360.0NaN0.000000NaNNaN0.0NaN...NaNNaNNaNNaN0.00.0NaN0.0000000.0000000.0
10497317NW_022994998.15494954951NaNNaNNaNNaNNaN0.0NaN...NaNNaNNaNNaNNaN0.0NaN0.0000000.0000000.0
10497318NW_022994998.15495354955NaNNaNNaNNaNNaN0.0NaN...NaNNaNNaNNaNNaN0.0NaN0.0000000.0000000.0
10497319NW_022994998.15495854960NaNNaNNaNNaNNaN0.0NaN...NaNNaNNaNNaNNaN0.0NaN0.0000000.0000000.0
\n", "

10 rows × 30 columns

\n", "
" ], "text/plain": [ " chrom start end 1 2 3 4 5 6 \\\n", "10497310 NW_022994998.1 54647 54649 0.0 0.0 9.090909 0.0 0.0 0.0 \n", "10497311 NW_022994998.1 54770 54772 0.0 0.0 0.000000 0.0 0.0 0.0 \n", "10497312 NW_022994998.1 54834 54836 0.0 0.0 0.000000 NaN 0.0 0.0 \n", "10497313 NW_022994998.1 54843 54845 0.0 NaN 0.000000 NaN 0.0 0.0 \n", "10497314 NW_022994998.1 54860 54862 0.0 NaN 0.000000 NaN 0.0 0.0 \n", "10497315 NW_022994998.1 54872 54874 0.0 NaN 0.000000 NaN 0.0 0.0 \n", "10497316 NW_022994998.1 54934 54936 0.0 NaN 0.000000 NaN NaN 0.0 \n", "10497317 NW_022994998.1 54949 54951 NaN NaN NaN NaN NaN 0.0 \n", "10497318 NW_022994998.1 54953 54955 NaN NaN NaN NaN NaN 0.0 \n", "10497319 NW_022994998.1 54958 54960 NaN NaN NaN NaN NaN 0.0 \n", "\n", " 7 ... 18 19 20 21 22 23 24 total \\\n", "10497310 0.0 ... 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.378788 \n", "10497311 0.0 ... 0.0 0.0 0.0 0.0 0.0 0.0 NaN 0.000000 \n", "10497312 0.0 ... 0.0 0.0 0.0 0.0 0.0 NaN NaN 0.000000 \n", "10497313 10.0 ... 0.0 0.0 0.0 0.0 0.0 NaN NaN 0.954545 \n", "10497314 0.0 ... 0.0 0.0 0.0 0.0 0.0 NaN NaN 0.000000 \n", "10497315 0.0 ... 0.0 0.0 0.0 0.0 0.0 NaN NaN 0.000000 \n", "10497316 NaN ... NaN NaN NaN NaN 0.0 0.0 NaN 0.000000 \n", "10497317 NaN ... NaN NaN NaN NaN NaN 0.0 NaN 0.000000 \n", "10497318 NaN ... NaN NaN NaN NaN NaN 0.0 NaN 0.000000 \n", "10497319 NaN ... NaN NaN NaN NaN NaN 0.0 NaN 0.000000 \n", "\n", " diploid triploid \n", "10497310 0.757576 0.0 \n", "10497311 0.000000 0.0 \n", "10497312 0.000000 0.0 \n", "10497313 1.909091 0.0 \n", "10497314 0.000000 0.0 \n", "10497315 0.000000 0.0 \n", "10497316 0.000000 0.0 \n", "10497317 0.000000 0.0 \n", "10497318 0.000000 0.0 \n", "10497319 0.000000 0.0 \n", "\n", "[10 rows x 30 columns]" ] }, "execution_count": 7, "metadata": {}, "output_type": "execute_result" } ], "source": [ "#Average all diploid samples and save as a new column\n", "#Average all triploid samples and save as a new column\n", "#NA are not included in averages\n", "#Check output\n", "df['diploid'] = df[['1', '2', '3', '4', '5', '6', '7', '8', '9', '10', '11', '12']].mean(axis=1)\n", "df['triploid'] = df[['13', '14', '15', '16', '17', '18', '19', '20', '21', '22', '23', '24']].mean(axis=1)\n", "df.tail(10)" ] }, { "cell_type": "code", "execution_count": 8, "metadata": { "collapsed": true }, "outputs": [], "source": [ "#Save dataframe in a tabular format and include N/As. Do not include quotes.\n", "df.to_csv(\"union-averages-ploidy.bedgraph\", sep = \"\\t\", na_rep = \"N/A\", quoting = 3)" ] }, { "cell_type": "code", "execution_count": 9, "metadata": { "collapsed": false, "scrolled": true }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "\tchrom\tstart\tend\t1\t2\t3\t4\t5\t6\t7\t8\t9\t10\t11\t12\t13\t14\t15\t16\t17\t18\t19\t20\t21\t22\t23\t24\ttotal\tdiploid\ttriploid\r\n", "0\tNC_001276.1\t34\t36\t3.092784\t1.162791\t3.061224\t3.401361\t3.6144580000000004\t2.659574\t4.375\t4.347826\t4.054054\t3.6036040000000003\t2.34375\t3.468208\t2.083333\t2.4539880000000003\t6.25\t5.479451999999999\t9.615385\t6.862744999999999\t5.217391\t1.785714\t2.150538\t3.3898309999999996\t2.380952\t5.303030000000001\t3.8398747083333338\t3.265386166666667\t4.41436325\r\n", "1\tNC_001276.1\t123\t125\t0.8510639999999999\t0.42553199999999997\t0.8264459999999999\t0.755668\t1.5625\t0.821355\t0.493827\t1.100917\t0.819672\t0.38759699999999997\t2.0066889999999997\t0.956938\t0.0\t0.512821\t1.115242\t1.020408\t0.378788\t0.396825\t1.689189\t0.727273\t1.1764709999999998\t0.845666\t1.287554\t1.3157889999999999\t0.894759625\t0.9173504166666665\t0.8721688333333333\r\n", "2\tNC_001276.1\t305\t307\t3.314917\t1.081081\t3.225806\t1.955307\t6.578947\t2.7397259999999997\t1.973684\t2.4038459999999997\t2.427184\t1.7777779999999999\t2.5252529999999997\t3.669725\t4.848485\t3.8461540000000003\t3.255814\t5.166052\t2.843602\t5.687204\t2.517986\t1.621622\t1.630435\t4.450262\t4.040404\t3.873239\t3.2272713749999995\t2.8061045\t3.64843825\r\n", "3\tNC_001276.1\t433\t435\t1.9867549999999998\t1.1673149999999999\t1.1331440000000002\t0.56926\t0.881057\t1.798561\t1.212121\t1.658375\t1.2924069999999999\t1.273885\t0.2849\t1.541426\t0.743494\t0.649351\t1.5625\t1.834862\t1.277955\t2.4734979999999998\t0.997506\t1.506024\t1.683502\t1.6806720000000002\t2.135231\t2.15311\t1.3957046250000003\t1.2332671666666666\t1.5581420833333333\r\n", "4\tNC_001276.1\t457\t459\t1.538462\t2.158273\t0.529101\t0.17211700000000002\t1.195219\t1.487603\t0.5607479999999999\t1.397516\t0.7656970000000001\t1.47929\t1.033592\t0.910747\t1.754386\t0.769231\t0.857143\t0.643777\t1.1594200000000001\t0.6191949999999999\t2.142857\t1.9830029999999998\t1.2383899999999999\t1.3740459999999999\t2.3178810000000003\t1.8306639999999998\t1.2465982500000001\t1.10236375\t1.3908327499999997\r\n", "5\tNC_001276.1\t482\t484\t0.6389779999999999\t2.076125\t1.749271\t0.743494\t0.0\t1.587302\t1.2422360000000001\t1.490066\t1.162791\t1.4285709999999998\t1.149425\t0.589391\t0.729927\t1.568627\t1.269841\t1.207729\t2.39521\t1.612903\t1.7902810000000002\t1.436782\t0.911854\t1.1764709999999998\t1.736111\t0.47732700000000006\t1.2571130416666667\t1.1548041666666666\t1.3594219166666663\r\n", "6\tNC_001276.1\t609\t611\t1.47929\t1.54321\t2.4258759999999997\t1.589825\t1.74216\t1.497006\t1.8761729999999999\t1.9230770000000001\t2.737752\t1.734104\t0.997506\t2.1015759999999997\t2.654867\t1.883562\t2.777778\t2.024291\t1.8372700000000002\t3.9548019999999995\t0.938967\t3.359173\t3.2\t2.352941\t2.8662419999999997\t1.716738\t2.1339244166666664\t1.8039629166666664\t2.4638859166666665\r\n", "7\tNC_001276.1\t781\t783\t1.457726\t1.298701\t1.941748\t1.37931\t2.2388060000000003\t1.121795\t1.7408119999999998\t3.153153\t2.489019\t2.7472529999999997\t2.843602\t1.325758\t1.597444\t1.449275\t3.651685\t1.8404909999999999\t1.608579\t2.295082\t1.9093080000000002\t2.2099450000000003\t2.727273\t3.74415\t3.508772\t1.434426\t2.1547547083333334\t1.9781402500000003\t2.3313691666666667\r\n", "8\tNC_001276.1\t826\t828\t1.346801\t2.205882\t2.298851\t0.200401\t0.823045\t2.1611\t0.8830020000000001\t2.117264\t1.036269\t1.7964069999999999\t0.831025\t1.237113\t1.37931\t1.131222\t1.010101\t1.345291\t1.333333\t1.503759\t0.8797649999999999\t1.577287\t1.048951\t2.2298459999999998\t1.8867919999999998\t1.162791\t1.3927336666666665\t1.4114300000000002\t1.3740373333333336\r\n" ] } ], "source": [ "#Check pandas manipulations\n", "!head union-averages-ploidy.bedgraph" ] }, { "cell_type": "code", "execution_count": 12, "metadata": { "collapsed": false }, "outputs": [], "source": [ "#Remove header\n", "#Keep chr, start, end, and the average\n", "#Save output\n", "! tail -n+2 union-averages-ploidy.bedgraph \\\n", "| awk -F'\\t' -v OFS='\\t' '{print $30, $31}' \\\n", "> ploidy-methylation-averages.bedgraph" ] }, { "cell_type": "code", "execution_count": 13, "metadata": { "collapsed": false, "scrolled": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "3.265386166666667\t4.41436325\n", "0.9173504166666665\t0.8721688333333333\n", "2.8061045\t3.64843825\n", "1.2332671666666666\t1.5581420833333333\n", "1.10236375\t1.3908327499999997\n", "1.1548041666666666\t1.3594219166666663\n", "1.8039629166666664\t2.4638859166666665\n", "1.9781402500000003\t2.3313691666666667\n", "1.4114300000000002\t1.3740373333333336\n", "3.294818\t3.372177\n", " 10497320 ploidy-methylation-averages.bedgraph\n" ] } ], "source": [ "#Check output: chr, start, end, average %meth\n", "!head ploidy-methylation-averages.bedgraph\n", "!wc -l ploidy-methylation-averages.bedgraph" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "## 4. Concatenate coverage information" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "As methylation detection relies on coverage, I want to understand potential coverage differences between diploids and triploids. This requires concatenating coverage information across samples." ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "### 4a. Format files" ] }, { "cell_type": "code", "execution_count": 19, "metadata": { "collapsed": true }, "outputs": [], "source": [ "%%bash\n", "\n", "for f in *cov\n", "do\n", " awk '{print $1\"\\t\"$2\"\\t\"$3\"\\t\"$5+$6}' ${f} \\\n", " > ${f}.txt\n", "done" ] }, { "cell_type": "code", "execution_count": 20, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "zr3644_10_R1_val_1_val_1_val_1_bismark_bt2_pe..CpG_report.merged_CpG_evidence.cov.txt\n", "zr3644_11_R1_val_1_val_1_val_1_bismark_bt2_pe..CpG_report.merged_CpG_evidence.cov.txt\n", "zr3644_12_R1_val_1_val_1_val_1_bismark_bt2_pe..CpG_report.merged_CpG_evidence.cov.txt\n", "zr3644_13_R1_val_1_val_1_val_1_bismark_bt2_pe..CpG_report.merged_CpG_evidence.cov.txt\n", "zr3644_14_R1_val_1_val_1_val_1_bismark_bt2_pe..CpG_report.merged_CpG_evidence.cov.txt\n", "zr3644_15_R1_val_1_val_1_val_1_bismark_bt2_pe..CpG_report.merged_CpG_evidence.cov.txt\n", "zr3644_16_R1_val_1_val_1_val_1_bismark_bt2_pe..CpG_report.merged_CpG_evidence.cov.txt\n", "zr3644_17_R1_val_1_val_1_val_1_bismark_bt2_pe..CpG_report.merged_CpG_evidence.cov.txt\n", "zr3644_18_R1_val_1_val_1_val_1_bismark_bt2_pe..CpG_report.merged_CpG_evidence.cov.txt\n", "zr3644_19_R1_val_1_val_1_val_1_bismark_bt2_pe..CpG_report.merged_CpG_evidence.cov.txt\n", "zr3644_1_R1_val_1_val_1_val_1_bismark_bt2_pe..CpG_report.merged_CpG_evidence.cov.txt\n", "zr3644_20_R1_val_1_val_1_val_1_bismark_bt2_pe..CpG_report.merged_CpG_evidence.cov.txt\n", "zr3644_21_R1_val_1_val_1_val_1_bismark_bt2_pe..CpG_report.merged_CpG_evidence.cov.txt\n", "zr3644_22_R1_val_1_val_1_val_1_bismark_bt2_pe..CpG_report.merged_CpG_evidence.cov.txt\n", "zr3644_23_R1_val_1_val_1_val_1_bismark_bt2_pe..CpG_report.merged_CpG_evidence.cov.txt\n", "zr3644_24_R1_val_1_val_1_val_1_bismark_bt2_pe..CpG_report.merged_CpG_evidence.cov.txt\n", "zr3644_2_R1_val_1_val_1_val_1_bismark_bt2_pe..CpG_report.merged_CpG_evidence.cov.txt\n", "zr3644_3_R1_val_1_val_1_val_1_bismark_bt2_pe..CpG_report.merged_CpG_evidence.cov.txt\n", "zr3644_4_R1_val_1_val_1_val_1_bismark_bt2_pe..CpG_report.merged_CpG_evidence.cov.txt\n", "zr3644_5_R1_val_1_val_1_val_1_bismark_bt2_pe..CpG_report.merged_CpG_evidence.cov.txt\n", "zr3644_6_R1_val_1_val_1_val_1_bismark_bt2_pe..CpG_report.merged_CpG_evidence.cov.txt\n", "zr3644_7_R1_val_1_val_1_val_1_bismark_bt2_pe..CpG_report.merged_CpG_evidence.cov.txt\n", "zr3644_8_R1_val_1_val_1_val_1_bismark_bt2_pe..CpG_report.merged_CpG_evidence.cov.txt\n", "zr3644_9_R1_val_1_val_1_val_1_bismark_bt2_pe..CpG_report.merged_CpG_evidence.cov.txt\n", "==> zr3644_10_R1_val_1_val_1_val_1_bismark_bt2_pe..CpG_report.merged_CpG_evidence.cov.txt <==\n", "NC_001276.1\t34\t36\t97\n", "NC_001276.1\t123\t125\t235\n", "NC_001276.1\t305\t307\t181\n", "NC_001276.1\t433\t435\t302\n", "NC_001276.1\t457\t459\t325\n", "NC_001276.1\t482\t484\t313\n", "NC_001276.1\t609\t611\t338\n", "NC_001276.1\t781\t783\t343\n", "NC_001276.1\t826\t828\t297\n", "NC_001276.1\t951\t953\t248\n", "\n", "==> zr3644_11_R1_val_1_val_1_val_1_bismark_bt2_pe..CpG_report.merged_CpG_evidence.cov.txt <==\n", "NC_001276.1\t34\t36\t86\n", "NC_001276.1\t123\t125\t235\n", "NC_001276.1\t305\t307\t185\n", "NC_001276.1\t433\t435\t257\n", "NC_001276.1\t457\t459\t278\n", "NC_001276.1\t482\t484\t289\n", "NC_001276.1\t609\t611\t324\n", "NC_001276.1\t781\t783\t308\n", "NC_001276.1\t826\t828\t272\n", "NC_001276.1\t951\t953\t224\n", "\n", "==> zr3644_12_R1_val_1_val_1_val_1_bismark_bt2_pe..CpG_report.merged_CpG_evidence.cov.txt <==\n", "NC_001276.1\t34\t36\t98\n", "NC_001276.1\t123\t125\t242\n", "NC_001276.1\t305\t307\t186\n", "NC_001276.1\t433\t435\t353\n", "NC_001276.1\t457\t459\t378\n", "NC_001276.1\t482\t484\t343\n", "NC_001276.1\t609\t611\t371\n", "NC_001276.1\t781\t783\t309\n", "NC_001276.1\t826\t828\t261\n", "NC_001276.1\t951\t953\t215\n", "\n", "==> zr3644_13_R1_val_1_val_1_val_1_bismark_bt2_pe..CpG_report.merged_CpG_evidence.cov.txt <==\n", "NC_001276.1\t34\t36\t147\n", "NC_001276.1\t123\t125\t397\n", "NC_001276.1\t305\t307\t358\n", "NC_001276.1\t433\t435\t527\n", "NC_001276.1\t457\t459\t581\n", "NC_001276.1\t482\t484\t538\n", "NC_001276.1\t609\t611\t629\n", "NC_001276.1\t781\t783\t580\n", "NC_001276.1\t826\t828\t499\n", "NC_001276.1\t951\t953\t390\n", "\n", "==> zr3644_14_R1_val_1_val_1_val_1_bismark_bt2_pe..CpG_report.merged_CpG_evidence.cov.txt <==\n", "NC_001276.1\t34\t36\t83\n", "NC_001276.1\t123\t125\t192\n", "NC_001276.1\t305\t307\t152\n", "NC_001276.1\t433\t435\t227\n", "NC_001276.1\t457\t459\t251\n", "NC_001276.1\t482\t484\t243\n", "NC_001276.1\t609\t611\t287\n", "NC_001276.1\t781\t783\t268\n", "NC_001276.1\t826\t828\t243\n", "NC_001276.1\t951\t953\t186\n", "\n", "==> zr3644_15_R1_val_1_val_1_val_1_bismark_bt2_pe..CpG_report.merged_CpG_evidence.cov.txt <==\n", "NC_001276.1\t34\t36\t188\n", "NC_001276.1\t123\t125\t487\n", "NC_001276.1\t305\t307\t365\n", "NC_001276.1\t433\t435\t556\n", "NC_001276.1\t457\t459\t605\n", "NC_001276.1\t482\t484\t567\n", "NC_001276.1\t609\t611\t668\n", "NC_001276.1\t781\t783\t624\n", "NC_001276.1\t826\t828\t509\n", "NC_001276.1\t951\t953\t424\n", "\n", "==> zr3644_16_R1_val_1_val_1_val_1_bismark_bt2_pe..CpG_report.merged_CpG_evidence.cov.txt <==\n", "NC_001276.1\t34\t36\t160\n", "NC_001276.1\t123\t125\t405\n", "NC_001276.1\t305\t307\t304\n", "NC_001276.1\t433\t435\t495\n", "NC_001276.1\t457\t459\t535\n", "NC_001276.1\t482\t484\t483\n", "NC_001276.1\t609\t611\t533\n", "NC_001276.1\t781\t783\t517\n", "NC_001276.1\t826\t828\t453\n", "NC_001276.1\t951\t953\t365\n", "\n", "==> zr3644_17_R1_val_1_val_1_val_1_bismark_bt2_pe..CpG_report.merged_CpG_evidence.cov.txt <==\n", "NC_001276.1\t34\t36\t207\n", "NC_001276.1\t123\t125\t545\n", "NC_001276.1\t305\t307\t416\n", "NC_001276.1\t433\t435\t603\n", "NC_001276.1\t457\t459\t644\n", "NC_001276.1\t482\t484\t604\n", "NC_001276.1\t609\t611\t676\n", "NC_001276.1\t781\t783\t666\n", "NC_001276.1\t826\t828\t614\n", "NC_001276.1\t951\t953\t430\n", "\n", "==> zr3644_18_R1_val_1_val_1_val_1_bismark_bt2_pe..CpG_report.merged_CpG_evidence.cov.txt <==\n", "NC_001276.1\t34\t36\t222\n", "NC_001276.1\t123\t125\t488\n", "NC_001276.1\t305\t307\t412\n", "NC_001276.1\t433\t435\t619\n", "NC_001276.1\t457\t459\t653\n", "NC_001276.1\t482\t484\t602\n", "NC_001276.1\t609\t611\t694\n", "NC_001276.1\t781\t783\t683\n", "NC_001276.1\t826\t828\t579\n", "NC_001276.1\t951\t953\t452\n", "\n", "==> zr3644_19_R1_val_1_val_1_val_1_bismark_bt2_pe..CpG_report.merged_CpG_evidence.cov.txt <==\n", "NC_001276.1\t34\t36\t111\n", "NC_001276.1\t123\t125\t258\n", "NC_001276.1\t305\t307\t225\n", "NC_001276.1\t433\t435\t314\n", "NC_001276.1\t457\t459\t338\n", "NC_001276.1\t482\t484\t280\n", "NC_001276.1\t609\t611\t346\n", "NC_001276.1\t781\t783\t364\n", "NC_001276.1\t826\t828\t334\n", "NC_001276.1\t951\t953\t219\n", "\n", "==> zr3644_1_R1_val_1_val_1_val_1_bismark_bt2_pe..CpG_report.merged_CpG_evidence.cov.txt <==\n", "NC_001276.1\t34\t36\t128\n", "NC_001276.1\t123\t125\t299\n", "NC_001276.1\t305\t307\t198\n", "NC_001276.1\t433\t435\t351\n", "NC_001276.1\t457\t459\t387\n", "NC_001276.1\t482\t484\t348\n", "NC_001276.1\t609\t611\t401\n", "NC_001276.1\t781\t783\t422\n", "NC_001276.1\t826\t828\t361\n", "NC_001276.1\t951\t953\t248\n", "\n", "==> zr3644_20_R1_val_1_val_1_val_1_bismark_bt2_pe..CpG_report.merged_CpG_evidence.cov.txt <==\n", "NC_001276.1\t34\t36\t173\n", "NC_001276.1\t123\t125\t418\n", "NC_001276.1\t305\t307\t327\n", "NC_001276.1\t433\t435\t519\n", "NC_001276.1\t457\t459\t549\n", "NC_001276.1\t482\t484\t509\n", "NC_001276.1\t609\t611\t571\n", "NC_001276.1\t781\t783\t528\n", "NC_001276.1\t826\t828\t485\n", "NC_001276.1\t951\t953\t394\n", "\n", "==> zr3644_21_R1_val_1_val_1_val_1_bismark_bt2_pe..CpG_report.merged_CpG_evidence.cov.txt <==\n", "NC_001276.1\t34\t36\t96\n", "NC_001276.1\t123\t125\t219\n", "NC_001276.1\t305\t307\t165\n", "NC_001276.1\t433\t435\t269\n", "NC_001276.1\t457\t459\t285\n", "NC_001276.1\t482\t484\t274\n", "NC_001276.1\t609\t611\t339\n", "NC_001276.1\t781\t783\t313\n", "NC_001276.1\t826\t828\t290\n", "NC_001276.1\t951\t953\t219\n", "\n", "==> zr3644_22_R1_val_1_val_1_val_1_bismark_bt2_pe..CpG_report.merged_CpG_evidence.cov.txt <==\n", "NC_001276.1\t34\t36\t163\n", "NC_001276.1\t123\t125\t390\n", "NC_001276.1\t305\t307\t338\n", "NC_001276.1\t433\t435\t462\n", "NC_001276.1\t457\t459\t520\n", "NC_001276.1\t482\t484\t510\n", "NC_001276.1\t609\t611\t584\n", "NC_001276.1\t781\t783\t483\n", "NC_001276.1\t826\t828\t442\n", "NC_001276.1\t951\t953\t391\n", "\n", "==> zr3644_23_R1_val_1_val_1_val_1_bismark_bt2_pe..CpG_report.merged_CpG_evidence.cov.txt <==\n", "NC_001276.1\t34\t36\t112\n", "NC_001276.1\t123\t125\t269\n", "NC_001276.1\t305\t307\t215\n", "NC_001276.1\t433\t435\t320\n", "NC_001276.1\t457\t459\t350\n", "NC_001276.1\t482\t484\t315\n", "NC_001276.1\t609\t611\t360\n", "NC_001276.1\t781\t783\t356\n", "NC_001276.1\t826\t828\t297\n", "NC_001276.1\t951\t953\t219\n", "\n", "==> zr3644_24_R1_val_1_val_1_val_1_bismark_bt2_pe..CpG_report.merged_CpG_evidence.cov.txt <==\n", "NC_001276.1\t34\t36\t146\n", "NC_001276.1\t123\t125\t392\n", "NC_001276.1\t305\t307\t271\n", "NC_001276.1\t433\t435\t436\n", "NC_001276.1\t457\t459\t466\n", "NC_001276.1\t482\t484\t414\n", "NC_001276.1\t609\t611\t494\n", "NC_001276.1\t781\t783\t489\n", "NC_001276.1\t826\t828\t446\n", "NC_001276.1\t951\t953\t303\n", "\n", "==> zr3644_2_R1_val_1_val_1_val_1_bismark_bt2_pe..CpG_report.merged_CpG_evidence.cov.txt <==\n", "NC_001276.1\t34\t36\t104\n", "NC_001276.1\t123\t125\t264\n", "NC_001276.1\t305\t307\t211\n", "NC_001276.1\t433\t435\t313\n", "NC_001276.1\t457\t459\t345\n", "NC_001276.1\t482\t484\t334\n", "NC_001276.1\t609\t611\t381\n", "NC_001276.1\t781\t783\t373\n", "NC_001276.1\t826\t828\t300\n", "NC_001276.1\t951\t953\t242\n", "\n", "==> zr3644_3_R1_val_1_val_1_val_1_bismark_bt2_pe..CpG_report.merged_CpG_evidence.cov.txt <==\n", "NC_001276.1\t34\t36\t102\n", "NC_001276.1\t123\t125\t252\n", "NC_001276.1\t305\t307\t211\n", "NC_001276.1\t433\t435\t283\n", "NC_001276.1\t457\t459\t323\n", "NC_001276.1\t482\t484\t310\n", "NC_001276.1\t609\t611\t354\n", "NC_001276.1\t781\t783\t305\n", "NC_001276.1\t826\t828\t266\n", "NC_001276.1\t951\t953\t224\n", "\n", "==> zr3644_4_R1_val_1_val_1_val_1_bismark_bt2_pe..CpG_report.merged_CpG_evidence.cov.txt <==\n", "NC_001276.1\t34\t36\t115\n", "NC_001276.1\t123\t125\t296\n", "NC_001276.1\t305\t307\t278\n", "NC_001276.1\t433\t435\t401\n", "NC_001276.1\t457\t459\t420\n", "NC_001276.1\t482\t484\t391\n", "NC_001276.1\t609\t611\t426\n", "NC_001276.1\t781\t783\t419\n", "NC_001276.1\t826\t828\t341\n", "NC_001276.1\t951\t953\t278\n", "\n", "==> zr3644_5_R1_val_1_val_1_val_1_bismark_bt2_pe..CpG_report.merged_CpG_evidence.cov.txt <==\n", "NC_001276.1\t34\t36\t112\n", "NC_001276.1\t123\t125\t275\n", "NC_001276.1\t305\t307\t185\n", "NC_001276.1\t433\t435\t332\n", "NC_001276.1\t457\t459\t353\n", "NC_001276.1\t482\t484\t348\n", "NC_001276.1\t609\t611\t387\n", "NC_001276.1\t781\t783\t362\n", "NC_001276.1\t826\t828\t317\n", "NC_001276.1\t951\t953\t247\n", "\n", "==> zr3644_6_R1_val_1_val_1_val_1_bismark_bt2_pe..CpG_report.merged_CpG_evidence.cov.txt <==\n", "NC_001276.1\t34\t36\t93\n", "NC_001276.1\t123\t125\t255\n", "NC_001276.1\t305\t307\t184\n", "NC_001276.1\t433\t435\t297\n", "NC_001276.1\t457\t459\t323\n", "NC_001276.1\t482\t484\t329\n", "NC_001276.1\t609\t611\t375\n", "NC_001276.1\t781\t783\t330\n", "NC_001276.1\t826\t828\t286\n", "NC_001276.1\t951\t953\t220\n", "\n", "==> zr3644_7_R1_val_1_val_1_val_1_bismark_bt2_pe..CpG_report.merged_CpG_evidence.cov.txt <==\n", "NC_001276.1\t34\t36\t177\n", "NC_001276.1\t123\t125\t473\n", "NC_001276.1\t305\t307\t382\n", "NC_001276.1\t433\t435\t595\n", "NC_001276.1\t457\t459\t655\n", "NC_001276.1\t482\t484\t595\n", "NC_001276.1\t609\t611\t680\n", "NC_001276.1\t781\t783\t641\n", "NC_001276.1\t826\t828\t583\n", "NC_001276.1\t951\t953\t494\n", "\n", "==> zr3644_8_R1_val_1_val_1_val_1_bismark_bt2_pe..CpG_report.merged_CpG_evidence.cov.txt <==\n", "NC_001276.1\t34\t36\t84\n", "NC_001276.1\t123\t125\t233\n", "NC_001276.1\t305\t307\t198\n", "NC_001276.1\t433\t435\t281\n", "NC_001276.1\t457\t459\t302\n", "NC_001276.1\t482\t484\t288\n", "NC_001276.1\t609\t611\t314\n", "NC_001276.1\t781\t783\t285\n", "NC_001276.1\t826\t828\t265\n", "NC_001276.1\t951\t953\t202\n", "\n", "==> zr3644_9_R1_val_1_val_1_val_1_bismark_bt2_pe..CpG_report.merged_CpG_evidence.cov.txt <==\n", "NC_001276.1\t34\t36\t132\n", "NC_001276.1\t123\t125\t380\n", "NC_001276.1\t305\t307\t284\n", "NC_001276.1\t433\t435\t418\n", "NC_001276.1\t457\t459\t437\n", "NC_001276.1\t482\t484\t419\n", "NC_001276.1\t609\t611\t466\n", "NC_001276.1\t781\t783\t488\n", "NC_001276.1\t826\t828\t430\n", "NC_001276.1\t951\t953\t333\n" ] } ], "source": [ "!find *cov.txt\n", "!head *cov.txt" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "### 4b. Create union coverage file" ] }, { "cell_type": "code", "execution_count": 21, "metadata": { "collapsed": true }, "outputs": [], "source": [ "%%bash\n", "\n", "for f in *cov.txt\n", "do\n", "/Users/Shared/bioinformatics/bedtools2/bin/sortBed \\\n", "-i ${f} \\\n", "> $(basename ${f%_cov.txt})_5x.sort.cov\n", "done" ] }, { "cell_type": "code", "execution_count": 22, "metadata": { "collapsed": false, "scrolled": true }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "zr3644_10_R1_val_1_val_1_val_1_bismark_bt2_pe..CpG_report.merged_CpG_evidence.cov.txt_5x.sort.cov\n", "zr3644_11_R1_val_1_val_1_val_1_bismark_bt2_pe..CpG_report.merged_CpG_evidence.cov.txt_5x.sort.cov\n", "zr3644_12_R1_val_1_val_1_val_1_bismark_bt2_pe..CpG_report.merged_CpG_evidence.cov.txt_5x.sort.cov\n", "zr3644_13_R1_val_1_val_1_val_1_bismark_bt2_pe..CpG_report.merged_CpG_evidence.cov.txt_5x.sort.cov\n", "zr3644_14_R1_val_1_val_1_val_1_bismark_bt2_pe..CpG_report.merged_CpG_evidence.cov.txt_5x.sort.cov\n", "zr3644_15_R1_val_1_val_1_val_1_bismark_bt2_pe..CpG_report.merged_CpG_evidence.cov.txt_5x.sort.cov\n", "zr3644_16_R1_val_1_val_1_val_1_bismark_bt2_pe..CpG_report.merged_CpG_evidence.cov.txt_5x.sort.cov\n", "zr3644_17_R1_val_1_val_1_val_1_bismark_bt2_pe..CpG_report.merged_CpG_evidence.cov.txt_5x.sort.cov\n", "zr3644_18_R1_val_1_val_1_val_1_bismark_bt2_pe..CpG_report.merged_CpG_evidence.cov.txt_5x.sort.cov\n", "zr3644_19_R1_val_1_val_1_val_1_bismark_bt2_pe..CpG_report.merged_CpG_evidence.cov.txt_5x.sort.cov\n", "zr3644_1_R1_val_1_val_1_val_1_bismark_bt2_pe..CpG_report.merged_CpG_evidence.cov.txt_5x.sort.cov\n", "zr3644_20_R1_val_1_val_1_val_1_bismark_bt2_pe..CpG_report.merged_CpG_evidence.cov.txt_5x.sort.cov\n", "zr3644_21_R1_val_1_val_1_val_1_bismark_bt2_pe..CpG_report.merged_CpG_evidence.cov.txt_5x.sort.cov\n", "zr3644_22_R1_val_1_val_1_val_1_bismark_bt2_pe..CpG_report.merged_CpG_evidence.cov.txt_5x.sort.cov\n", "zr3644_23_R1_val_1_val_1_val_1_bismark_bt2_pe..CpG_report.merged_CpG_evidence.cov.txt_5x.sort.cov\n", "zr3644_24_R1_val_1_val_1_val_1_bismark_bt2_pe..CpG_report.merged_CpG_evidence.cov.txt_5x.sort.cov\n", "zr3644_2_R1_val_1_val_1_val_1_bismark_bt2_pe..CpG_report.merged_CpG_evidence.cov.txt_5x.sort.cov\n", "zr3644_3_R1_val_1_val_1_val_1_bismark_bt2_pe..CpG_report.merged_CpG_evidence.cov.txt_5x.sort.cov\n", "zr3644_4_R1_val_1_val_1_val_1_bismark_bt2_pe..CpG_report.merged_CpG_evidence.cov.txt_5x.sort.cov\n", "zr3644_5_R1_val_1_val_1_val_1_bismark_bt2_pe..CpG_report.merged_CpG_evidence.cov.txt_5x.sort.cov\n", "zr3644_6_R1_val_1_val_1_val_1_bismark_bt2_pe..CpG_report.merged_CpG_evidence.cov.txt_5x.sort.cov\n", "zr3644_7_R1_val_1_val_1_val_1_bismark_bt2_pe..CpG_report.merged_CpG_evidence.cov.txt_5x.sort.cov\n", "zr3644_8_R1_val_1_val_1_val_1_bismark_bt2_pe..CpG_report.merged_CpG_evidence.cov.txt_5x.sort.cov\n", "zr3644_9_R1_val_1_val_1_val_1_bismark_bt2_pe..CpG_report.merged_CpG_evidence.cov.txt_5x.sort.cov\n" ] } ], "source": [ "!ls *sort*" ] }, { "cell_type": "code", "execution_count": 25, "metadata": { "collapsed": false }, "outputs": [], "source": [ "#Create union BEDgraph from sorted files\n", "#Include a header\n", "#Use N/A when there is no data for a CpG in a sample\n", "#Define sample IDs\n", "#Use sorted bedgraphs\n", "#Save output\n", "!{bedtoolsDirectory}unionBedGraphs \\\n", "-header \\\n", "-filler N/A \\\n", "-names 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 \\\n", "-i \\\n", "*5x.sort.cov \\\n", "> union_5x.cov" ] }, { "cell_type": "code", "execution_count": 26, "metadata": { "collapsed": false, "scrolled": true }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "chrom\tstart\tend\t1\t2\t3\t4\t5\t6\t7\t8\t9\t10\t11\t12\t13\t14\t15\t16\t17\t18\t19\t20\t21\t22\t23\t24\n", "NC_001276.1\t34\t36\t97\t86\t98\t147\t83\t188\t160\t207\t222\t111\t128\t173\t96\t163\t112\t146\t104\t102\t115\t112\t93\t177\t84\t132\n", "NC_001276.1\t123\t125\t235\t235\t242\t397\t192\t487\t405\t545\t488\t258\t299\t418\t219\t390\t269\t392\t264\t252\t296\t275\t255\t473\t233\t380\n", "NC_001276.1\t305\t307\t181\t185\t186\t358\t152\t365\t304\t416\t412\t225\t198\t327\t165\t338\t215\t271\t211\t211\t278\t185\t184\t382\t198\t284\n", "NC_001276.1\t433\t435\t302\t257\t353\t527\t227\t556\t495\t603\t619\t314\t351\t519\t269\t462\t320\t436\t313\t283\t401\t332\t297\t595\t281\t418\n", "NC_001276.1\t457\t459\t325\t278\t378\t581\t251\t605\t535\t644\t653\t338\t387\t549\t285\t520\t350\t466\t345\t323\t420\t353\t323\t655\t302\t437\n", "NC_001276.1\t482\t484\t313\t289\t343\t538\t243\t567\t483\t604\t602\t280\t348\t509\t274\t510\t315\t414\t334\t310\t391\t348\t329\t595\t288\t419\n", "NC_001276.1\t609\t611\t338\t324\t371\t629\t287\t668\t533\t676\t694\t346\t401\t571\t339\t584\t360\t494\t381\t354\t426\t387\t375\t680\t314\t466\n", "NC_001276.1\t781\t783\t343\t308\t309\t580\t268\t624\t517\t666\t683\t364\t422\t528\t313\t483\t356\t489\t373\t305\t419\t362\t330\t641\t285\t488\n", "NC_001276.1\t826\t828\t297\t272\t261\t499\t243\t509\t453\t614\t579\t334\t361\t485\t290\t442\t297\t446\t300\t266\t341\t317\t286\t583\t265\t430\n", " 12794075 union_5x.cov\n" ] } ], "source": [ "#Check output\n", "!head union_5x.cov\n", "!wc -l union_5x.cov" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "### 4c. Manipulate with `pandas`" ] }, { "cell_type": "code", "execution_count": 27, "metadata": { "collapsed": false }, "outputs": [ { "data": { "text/html": [ "
\n", "\n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", "
chromstartend1234567...15161718192021222324
0NC_001276.1343697.086.098.0147.083.0188.0160.0...112.0146.0104.0102.0115.0112.093.0177.084.0132.0
1NC_001276.1123125235.0235.0242.0397.0192.0487.0405.0...269.0392.0264.0252.0296.0275.0255.0473.0233.0380.0
2NC_001276.1305307181.0185.0186.0358.0152.0365.0304.0...215.0271.0211.0211.0278.0185.0184.0382.0198.0284.0
3NC_001276.1433435302.0257.0353.0527.0227.0556.0495.0...320.0436.0313.0283.0401.0332.0297.0595.0281.0418.0
4NC_001276.1457459325.0278.0378.0581.0251.0605.0535.0...350.0466.0345.0323.0420.0353.0323.0655.0302.0437.0
\n", "

5 rows × 27 columns

\n", "
" ], "text/plain": [ " chrom start end 1 2 3 4 5 6 7 \\\n", "0 NC_001276.1 34 36 97.0 86.0 98.0 147.0 83.0 188.0 160.0 \n", "1 NC_001276.1 123 125 235.0 235.0 242.0 397.0 192.0 487.0 405.0 \n", "2 NC_001276.1 305 307 181.0 185.0 186.0 358.0 152.0 365.0 304.0 \n", "3 NC_001276.1 433 435 302.0 257.0 353.0 527.0 227.0 556.0 495.0 \n", "4 NC_001276.1 457 459 325.0 278.0 378.0 581.0 251.0 605.0 535.0 \n", "\n", " ... 15 16 17 18 19 20 21 22 23 24 \n", "0 ... 112.0 146.0 104.0 102.0 115.0 112.0 93.0 177.0 84.0 132.0 \n", "1 ... 269.0 392.0 264.0 252.0 296.0 275.0 255.0 473.0 233.0 380.0 \n", "2 ... 215.0 271.0 211.0 211.0 278.0 185.0 184.0 382.0 198.0 284.0 \n", "3 ... 320.0 436.0 313.0 283.0 401.0 332.0 297.0 595.0 281.0 418.0 \n", "4 ... 350.0 466.0 345.0 323.0 420.0 353.0 323.0 655.0 302.0 437.0 \n", "\n", "[5 rows x 27 columns]" ] }, "execution_count": 27, "metadata": {}, "output_type": "execute_result" } ], "source": [ "#Import union data into pandas\n", "#Check head\n", "df = pd.read_table(\"union_5x.cov\")\n", "df.head(5)" ] }, { "cell_type": "code", "execution_count": 28, "metadata": { "collapsed": false, "scrolled": true }, "outputs": [ { "data": { "text/html": [ "
\n", "\n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", "
chromstartend1234567...1718192021222324diploidtriploid
12794064NW_022994998.154834548367.05.013.03.08.07.010.0...6.05.07.08.06.014.04.02.08.0833337.000000
12794065NW_022994998.154843548457.04.012.04.08.07.010.0...6.05.07.08.06.012.04.03.08.0000006.833333
12794066NW_022994998.154860548625.04.012.03.07.06.011.0...6.06.07.06.06.014.04.03.07.4166676.833333
12794067NW_022994998.154872548745.04.011.02.07.06.08.0...6.06.06.06.06.013.04.03.06.5833336.333333
12794068NW_022994998.154934549366.02.05.02.03.07.03.0...3.04.02.02.02.05.05.01.04.1818182.916667
12794069NW_022994998.154949549514.02.03.01.02.06.02.0...1.04.02.01.02.03.05.01.02.9090912.500000
12794070NW_022994998.154953549552.02.03.01.02.06.02.0...1.03.02.01.02.03.05.01.02.6363642.363636
12794071NW_022994998.154958549602.02.03.01.02.06.02.0...1.03.02.01.02.03.05.01.02.6363642.272727
12794072NW_022994998.15500155003NaN1.01.01.01.04.0NaN...NaN1.0NaNNaNNaN3.02.0NaN1.6000001.600000
12794073NW_022994998.15502655028NaN1.0NaNNaNNaNNaNNaN...NaNNaNNaNNaNNaNNaNNaNNaN1.0000001.000000
\n", "

10 rows × 29 columns

\n", "
" ], "text/plain": [ " chrom start end 1 2 3 4 5 6 7 \\\n", "12794064 NW_022994998.1 54834 54836 7.0 5.0 13.0 3.0 8.0 7.0 10.0 \n", "12794065 NW_022994998.1 54843 54845 7.0 4.0 12.0 4.0 8.0 7.0 10.0 \n", "12794066 NW_022994998.1 54860 54862 5.0 4.0 12.0 3.0 7.0 6.0 11.0 \n", "12794067 NW_022994998.1 54872 54874 5.0 4.0 11.0 2.0 7.0 6.0 8.0 \n", "12794068 NW_022994998.1 54934 54936 6.0 2.0 5.0 2.0 3.0 7.0 3.0 \n", "12794069 NW_022994998.1 54949 54951 4.0 2.0 3.0 1.0 2.0 6.0 2.0 \n", "12794070 NW_022994998.1 54953 54955 2.0 2.0 3.0 1.0 2.0 6.0 2.0 \n", "12794071 NW_022994998.1 54958 54960 2.0 2.0 3.0 1.0 2.0 6.0 2.0 \n", "12794072 NW_022994998.1 55001 55003 NaN 1.0 1.0 1.0 1.0 4.0 NaN \n", "12794073 NW_022994998.1 55026 55028 NaN 1.0 NaN NaN NaN NaN NaN \n", "\n", " ... 17 18 19 20 21 22 23 24 diploid \\\n", "12794064 ... 6.0 5.0 7.0 8.0 6.0 14.0 4.0 2.0 8.083333 \n", "12794065 ... 6.0 5.0 7.0 8.0 6.0 12.0 4.0 3.0 8.000000 \n", "12794066 ... 6.0 6.0 7.0 6.0 6.0 14.0 4.0 3.0 7.416667 \n", "12794067 ... 6.0 6.0 6.0 6.0 6.0 13.0 4.0 3.0 6.583333 \n", "12794068 ... 3.0 4.0 2.0 2.0 2.0 5.0 5.0 1.0 4.181818 \n", "12794069 ... 1.0 4.0 2.0 1.0 2.0 3.0 5.0 1.0 2.909091 \n", "12794070 ... 1.0 3.0 2.0 1.0 2.0 3.0 5.0 1.0 2.636364 \n", "12794071 ... 1.0 3.0 2.0 1.0 2.0 3.0 5.0 1.0 2.636364 \n", "12794072 ... NaN 1.0 NaN NaN NaN 3.0 2.0 NaN 1.600000 \n", "12794073 ... NaN NaN NaN NaN NaN NaN NaN NaN 1.000000 \n", "\n", " triploid \n", "12794064 7.000000 \n", "12794065 6.833333 \n", "12794066 6.833333 \n", "12794067 6.333333 \n", "12794068 2.916667 \n", "12794069 2.500000 \n", "12794070 2.363636 \n", "12794071 2.272727 \n", "12794072 1.600000 \n", "12794073 1.000000 \n", "\n", "[10 rows x 29 columns]" ] }, "execution_count": 28, "metadata": {}, "output_type": "execute_result" } ], "source": [ "#Average all diploid samples and save as a new column\n", "#Average all triploid samples and save as a new column\n", "#NA are not included in averages\n", "#Check output\n", "df['diploid'] = df[['1', '2', '3', '4', '5', '6', '7', '8', '9', '10', '11', '12']].mean(axis=1)\n", "df['triploid'] = df[['13', '14', '15', '16', '17', '18', '19', '20', '21', '22', '23', '24']].mean(axis=1)\n", "df.tail(10)" ] }, { "cell_type": "code", "execution_count": 29, "metadata": { "collapsed": true }, "outputs": [], "source": [ "#Save dataframe in a tabular format and include N/As. Do not include quotes.\n", "df.to_csv(\"union-cov-ploidy.bedgraph\", sep = \"\\t\", na_rep = \"N/A\", quoting = 3)" ] }, { "cell_type": "code", "execution_count": 30, "metadata": { "collapsed": false, "scrolled": true }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "\tchrom\tstart\tend\t1\t2\t3\t4\t5\t6\t7\t8\t9\t10\t11\t12\t13\t14\t15\t16\t17\t18\t19\t20\t21\t22\t23\t24\tdiploid\ttriploid\r\n", "0\tNC_001276.1\t34\t36\t97.0\t86.0\t98.0\t147.0\t83.0\t188.0\t160.0\t207.0\t222.0\t111.0\t128.0\t173.0\t96.0\t163.0\t112.0\t146.0\t104.0\t102.0\t115.0\t112.0\t93.0\t177.0\t84.0\t132.0\t141.66666666666666\t119.66666666666667\r\n", "1\tNC_001276.1\t123\t125\t235.0\t235.0\t242.0\t397.0\t192.0\t487.0\t405.0\t545.0\t488.0\t258.0\t299.0\t418.0\t219.0\t390.0\t269.0\t392.0\t264.0\t252.0\t296.0\t275.0\t255.0\t473.0\t233.0\t380.0\t350.0833333333333\t308.1666666666667\r\n", "2\tNC_001276.1\t305\t307\t181.0\t185.0\t186.0\t358.0\t152.0\t365.0\t304.0\t416.0\t412.0\t225.0\t198.0\t327.0\t165.0\t338.0\t215.0\t271.0\t211.0\t211.0\t278.0\t185.0\t184.0\t382.0\t198.0\t284.0\t275.75\t243.5\r\n", "3\tNC_001276.1\t433\t435\t302.0\t257.0\t353.0\t527.0\t227.0\t556.0\t495.0\t603.0\t619.0\t314.0\t351.0\t519.0\t269.0\t462.0\t320.0\t436.0\t313.0\t283.0\t401.0\t332.0\t297.0\t595.0\t281.0\t418.0\t426.9166666666667\t367.25\r\n", "4\tNC_001276.1\t457\t459\t325.0\t278.0\t378.0\t581.0\t251.0\t605.0\t535.0\t644.0\t653.0\t338.0\t387.0\t549.0\t285.0\t520.0\t350.0\t466.0\t345.0\t323.0\t420.0\t353.0\t323.0\t655.0\t302.0\t437.0\t460.3333333333333\t398.25\r\n", "5\tNC_001276.1\t482\t484\t313.0\t289.0\t343.0\t538.0\t243.0\t567.0\t483.0\t604.0\t602.0\t280.0\t348.0\t509.0\t274.0\t510.0\t315.0\t414.0\t334.0\t310.0\t391.0\t348.0\t329.0\t595.0\t288.0\t419.0\t426.5833333333333\t377.25\r\n", "6\tNC_001276.1\t609\t611\t338.0\t324.0\t371.0\t629.0\t287.0\t668.0\t533.0\t676.0\t694.0\t346.0\t401.0\t571.0\t339.0\t584.0\t360.0\t494.0\t381.0\t354.0\t426.0\t387.0\t375.0\t680.0\t314.0\t466.0\t486.5\t430.0\r\n", "7\tNC_001276.1\t781\t783\t343.0\t308.0\t309.0\t580.0\t268.0\t624.0\t517.0\t666.0\t683.0\t364.0\t422.0\t528.0\t313.0\t483.0\t356.0\t489.0\t373.0\t305.0\t419.0\t362.0\t330.0\t641.0\t285.0\t488.0\t467.6666666666667\t403.6666666666667\r\n", "8\tNC_001276.1\t826\t828\t297.0\t272.0\t261.0\t499.0\t243.0\t509.0\t453.0\t614.0\t579.0\t334.0\t361.0\t485.0\t290.0\t442.0\t297.0\t446.0\t300.0\t266.0\t341.0\t317.0\t286.0\t583.0\t265.0\t430.0\t408.9166666666667\t355.25\r\n" ] } ], "source": [ "#Check pandas manipulations\n", "!head union-cov-ploidy.bedgraph" ] }, { "cell_type": "code", "execution_count": 31, "metadata": { "collapsed": false }, "outputs": [], "source": [ "#Remove header\n", "#Keep chr, start, end, and the average\n", "#Save output\n", "! tail -n+2 union-cov-ploidy.bedgraph \\\n", "| awk -F'\\t' -v OFS='\\t' '{print $29, $30}' \\\n", "> ploidy-cov-averages.bedgraph" ] }, { "cell_type": "code", "execution_count": 32, "metadata": { "collapsed": false, "scrolled": true }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "141.66666666666666\t119.66666666666667\n", "350.0833333333333\t308.1666666666667\n", "275.75\t243.5\n", "426.9166666666667\t367.25\n", "460.3333333333333\t398.25\n", "426.5833333333333\t377.25\n", "486.5\t430.0\n", "467.6666666666667\t403.6666666666667\n", "408.9166666666667\t355.25\n", "316.25\t281.0\n", " 12794074 ploidy-cov-averages.bedgraph\n" ] } ], "source": [ "#Check output: chr, start, end, average %meth\n", "!head ploidy-cov-averages.bedgraph\n", "!wc -l ploidy-cov-averages.bedgraph" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "## 5. Characterize methylation for each CpG dinucleotude" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "- methylated: ≥ 50%\n", "- sparsely methylated: 10-50%\n", "- unmethylated: ≤ 10%" ] }, { "cell_type": "code", "execution_count": 21, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "zr3644_10_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph\r\n", "zr3644_11_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph\r\n", "zr3644_12_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph\r\n", "zr3644_13_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph\r\n", "zr3644_14_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph\r\n", "zr3644_15_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph\r\n", "zr3644_16_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph\r\n", "zr3644_17_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph\r\n", "zr3644_18_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph\r\n", "zr3644_19_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph\r\n", "zr3644_1_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph\r\n", "zr3644_20_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph\r\n", "zr3644_21_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph\r\n", "zr3644_22_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph\r\n", "zr3644_23_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph\r\n", "zr3644_24_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph\r\n", "zr3644_2_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph\r\n", "zr3644_3_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph\r\n", "zr3644_4_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph\r\n", "zr3644_5_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph\r\n", "zr3644_6_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph\r\n", "zr3644_7_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph\r\n", "zr3644_8_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph\r\n", "zr3644_9_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph\r\n", "zr3644_union-averages_5x.bedgraph\r\n" ] } ], "source": [ "#8 individual sample files + 1 union bedgraph\n", "!find zr3644*5x.bedgraph" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "### 5a. Methylated loci" ] }, { "cell_type": "code", "execution_count": 22, "metadata": { "collapsed": true }, "outputs": [], "source": [ "%%bash\n", "for f in zr3644*5x.bedgraph\n", "do\n", " awk '{if ($4 >= 50) { print $1, $2, $3, $4 }}' ${f} \\\n", " > ${f}-Meth\n", "done" ] }, { "cell_type": "code", "execution_count": 23, "metadata": { "collapsed": false, "scrolled": true }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "==> zr3644_10_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth <==\n", "NC_047559.1 4270 4272 50.000000\n", "NC_047559.1 4791 4793 68.750000\n", "NC_047559.1 4835 4837 88.888889\n", "NC_047559.1 4843 4845 91.304348\n", "NC_047559.1 4887 4889 80.000000\n", "NC_047559.1 7490 7492 93.750000\n", "NC_047559.1 7671 7673 83.333333\n", "NC_047559.1 7814 7816 60.000000\n", "NC_047559.1 7850 7852 62.500000\n", "NC_047559.1 7867 7869 77.777778\n", "\n", "==> zr3644_11_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth <==\n", "NC_047559.1 4843 4845 65.384615\n", "NC_047559.1 4887 4889 58.333333\n", "NC_047559.1 5316 5318 57.142857\n", "NC_047559.1 7129 7131 96.551724\n", "NC_047559.1 7490 7492 84.615385\n", "NC_047559.1 7671 7673 90.909091\n", "NC_047559.1 7814 7816 75.000000\n", "NC_047559.1 7850 7852 75.000000\n", "NC_047559.1 7867 7869 95.238095\n", "NC_047559.1 7885 7887 76.470588\n", "\n", "==> zr3644_12_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth <==\n", "NC_047559.1 4791 4793 53.125000\n", "NC_047559.1 4835 4837 68.421053\n", "NC_047559.1 4843 4845 68.421053\n", "NC_047559.1 4887 4889 60.000000\n", "NC_047559.1 7671 7673 85.714286\n", "NC_047559.1 7814 7816 77.777778\n", "NC_047559.1 7850 7852 92.307692\n", "NC_047559.1 7867 7869 90.909091\n", "NC_047559.1 7885 7887 88.888889\n", "NC_047559.1 9122 9124 66.666667\n", "\n", "==> zr3644_13_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth <==\n", "NC_047559.1 4791 4793 57.446809\n", "NC_047559.1 4835 4837 68.750000\n", "NC_047559.1 4843 4845 67.857143\n", "NC_047559.1 4909 4911 50.000000\n", "NC_047559.1 6486 6488 80.000000\n", "NC_047559.1 6492 6494 60.000000\n", "NC_047559.1 7129 7131 60.000000\n", "NC_047559.1 7490 7492 71.428571\n", "NC_047559.1 7671 7673 58.333333\n", "NC_047559.1 7814 7816 92.857143\n", "\n", "==> zr3644_14_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth <==\n", "NC_047559.1 4791 4793 87.500000\n", "NC_047559.1 4835 4837 100.000000\n", "NC_047559.1 4843 4845 100.000000\n", "NC_047559.1 24926 24928 50.000000\n", "NC_047559.1 24932 24934 50.000000\n", "NC_047559.1 24934 24936 50.000000\n", "NC_047559.1 62770 62772 50.000000\n", "NC_047559.1 68070 68072 100.000000\n", "NC_047559.1 164604 164606 62.500000\n", "NC_047559.1 164626 164628 62.500000\n", "\n", "==> zr3644_15_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth <==\n", "NC_047559.1 4791 4793 65.116279\n", "NC_047559.1 4835 4837 88.235294\n", "NC_047559.1 4843 4845 81.818182\n", "NC_047559.1 4887 4889 86.666667\n", "NC_047559.1 4909 4911 71.428571\n", "NC_047559.1 5316 5318 60.000000\n", "NC_047559.1 5605 5607 57.142857\n", "NC_047559.1 5613 5615 66.666667\n", "NC_047559.1 7129 7131 92.857143\n", "NC_047559.1 7490 7492 85.185185\n", "\n", "==> zr3644_16_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth <==\n", "NC_047559.1 4791 4793 75.000000\n", "NC_047559.1 4835 4837 83.870968\n", "NC_047559.1 4843 4845 92.857143\n", "NC_047559.1 4887 4889 91.666667\n", "NC_047559.1 4909 4911 85.714286\n", "NC_047559.1 7129 7131 68.421053\n", "NC_047559.1 7490 7492 75.000000\n", "NC_047559.1 7671 7673 78.571429\n", "NC_047559.1 7814 7816 80.000000\n", "NC_047559.1 7850 7852 91.666667\n", "\n", "==> zr3644_17_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth <==\n", "NC_047559.1 4791 4793 55.357143\n", "NC_047559.1 4835 4837 91.489362\n", "NC_047559.1 4843 4845 89.361702\n", "NC_047559.1 4887 4889 91.304348\n", "NC_047559.1 5613 5615 62.500000\n", "NC_047559.1 7490 7492 66.666667\n", "NC_047559.1 24066 24068 60.000000\n", "NC_047559.1 44918 44920 60.000000\n", "NC_047559.1 147333 147335 50.000000\n", "NC_047559.1 147335 147337 50.000000\n", "\n", "==> zr3644_18_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth <==\n", "NC_047559.1 4835 4837 52.380952\n", "NC_047559.1 4843 4845 60.526316\n", "NC_047559.1 4909 4911 50.000000\n", "NC_047559.1 5500 5502 55.555556\n", "NC_047559.1 7129 7131 66.666667\n", "NC_047559.1 7490 7492 76.470588\n", "NC_047559.1 7671 7673 71.428571\n", "NC_047559.1 7850 7852 66.666667\n", "NC_047559.1 7867 7869 100.000000\n", "NC_047559.1 7885 7887 80.000000\n", "\n", "==> zr3644_19_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth <==\n", "NC_047559.1 4835 4837 57.142857\n", "NC_047559.1 4843 4845 60.000000\n", "NC_047559.1 4887 4889 73.333333\n", "NC_047559.1 4909 4911 57.142857\n", "NC_047559.1 7129 7131 82.608696\n", "NC_047559.1 7490 7492 83.333333\n", "NC_047559.1 7671 7673 60.000000\n", "NC_047559.1 7814 7816 100.000000\n", "NC_047559.1 7850 7852 83.333333\n", "NC_047559.1 7867 7869 100.000000\n", "\n", "==> zr3644_1_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth <==\n", "NC_047559.1 2267 2269 100.000000\n", "NC_047559.1 2291 2293 87.500000\n", "NC_047559.1 4791 4793 69.230769\n", "NC_047559.1 4835 4837 100.000000\n", "NC_047559.1 4843 4845 90.000000\n", "NC_047559.1 7129 7131 85.714286\n", "NC_047559.1 7490 7492 57.142857\n", "NC_047559.1 7885 7887 80.000000\n", "NC_047559.1 7923 7925 66.666667\n", "NC_047559.1 7939 7941 80.000000\n", "\n", "==> zr3644_20_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth <==\n", "NC_047559.1 4397 4399 60.000000\n", "NC_047559.1 4843 4845 50.000000\n", "NC_047559.1 5605 5607 50.000000\n", "NC_047559.1 7129 7131 65.384615\n", "NC_047559.1 7490 7492 75.000000\n", "NC_047559.1 7671 7673 100.000000\n", "NC_047559.1 7814 7816 91.666667\n", "NC_047559.1 7850 7852 100.000000\n", "NC_047559.1 7867 7869 100.000000\n", "NC_047559.1 7885 7887 100.000000\n", "\n", "==> zr3644_21_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth <==\n", "NC_047559.1 4791 4793 65.517241\n", "NC_047559.1 4835 4837 79.166667\n", "NC_047559.1 4843 4845 77.272727\n", "NC_047559.1 4887 4889 90.909091\n", "NC_047559.1 4909 4911 87.500000\n", "NC_047559.1 7129 7131 90.000000\n", "NC_047559.1 7490 7492 74.074074\n", "NC_047559.1 7671 7673 70.000000\n", "NC_047559.1 7814 7816 85.714286\n", "NC_047559.1 7850 7852 77.777778\n", "\n", "==> zr3644_22_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth <==\n", "NC_047559.1 4791 4793 61.290323\n", "NC_047559.1 4835 4837 83.333333\n", "NC_047559.1 4843 4845 95.652174\n", "NC_047559.1 4887 4889 83.333333\n", "NC_047559.1 4909 4911 50.000000\n", "NC_047559.1 5605 5607 50.000000\n", "NC_047559.1 7129 7131 77.777778\n", "NC_047559.1 7490 7492 64.285714\n", "NC_047559.1 7671 7673 88.888889\n", "NC_047559.1 7814 7816 100.000000\n", "\n", "==> zr3644_23_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth <==\n", "NC_047559.1 4835 4837 61.538462\n", "NC_047559.1 4843 4845 69.565217\n", "NC_047559.1 4887 4889 70.000000\n", "NC_047559.1 7129 7131 85.714286\n", "NC_047559.1 7490 7492 78.571429\n", "NC_047559.1 7671 7673 100.000000\n", "NC_047559.1 7814 7816 100.000000\n", "NC_047559.1 7850 7852 100.000000\n", "NC_047559.1 7867 7869 83.333333\n", "NC_047559.1 7885 7887 92.857143\n", "\n", "==> zr3644_24_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth <==\n", "NC_047559.1 1571 1573 83.333333\n", "NC_047559.1 4835 4837 56.000000\n", "NC_047559.1 4843 4845 68.000000\n", "NC_047559.1 4887 4889 68.750000\n", "NC_047559.1 4909 4911 54.545455\n", "NC_047559.1 7129 7131 81.818182\n", "NC_047559.1 7490 7492 88.235294\n", "NC_047559.1 7671 7673 87.500000\n", "NC_047559.1 7814 7816 77.777778\n", "NC_047559.1 7850 7852 80.000000\n", "\n", "==> zr3644_2_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth <==\n", "NC_047559.1 4073 4075 60.000000\n", "NC_047559.1 4791 4793 65.116279\n", "NC_047559.1 4835 4837 76.923077\n", "NC_047559.1 4843 4845 78.378378\n", "NC_047559.1 4887 4889 83.333333\n", "NC_047559.1 4909 4911 56.250000\n", "NC_047559.1 5500 5502 60.000000\n", "NC_047559.1 7129 7131 57.142857\n", "NC_047559.1 7490 7492 88.888889\n", "NC_047559.1 7671 7673 90.000000\n", "\n", "==> zr3644_3_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth <==\n", "NC_047559.1 4791 4793 57.142857\n", "NC_047559.1 4835 4837 63.636364\n", "NC_047559.1 4843 4845 65.217391\n", "NC_047559.1 4887 4889 70.000000\n", "NC_047559.1 7129 7131 100.000000\n", "NC_047559.1 7490 7492 76.923077\n", "NC_047559.1 7671 7673 100.000000\n", "NC_047559.1 7716 7718 83.333333\n", "NC_047559.1 7814 7816 80.000000\n", "NC_047559.1 7867 7869 100.000000\n", "\n", "==> zr3644_4_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth <==\n", "NC_047559.1 4073 4075 71.428571\n", "NC_047559.1 4270 4272 50.000000\n", "NC_047559.1 4887 4889 50.000000\n", "NC_047559.1 4909 4911 66.666667\n", "NC_047559.1 7129 7131 81.250000\n", "NC_047559.1 7490 7492 61.904762\n", "NC_047559.1 7671 7673 80.000000\n", "NC_047559.1 7814 7816 83.333333\n", "NC_047559.1 7850 7852 75.000000\n", "NC_047559.1 7867 7869 88.888889\n", "\n", "==> zr3644_5_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth <==\n", "NC_047559.1 4791 4793 75.000000\n", "NC_047559.1 4835 4837 94.736842\n", "NC_047559.1 4843 4845 94.736842\n", "NC_047559.1 4887 4889 100.000000\n", "NC_047559.1 4909 4911 60.000000\n", "NC_047559.1 7129 7131 70.833333\n", "NC_047559.1 7490 7492 72.222222\n", "NC_047559.1 7671 7673 90.909091\n", "NC_047559.1 7814 7816 55.555556\n", "NC_047559.1 7850 7852 88.888889\n", "\n", "==> zr3644_6_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth <==\n", "NC_047559.1 2087 2089 60.000000\n", "NC_047559.1 4835 4837 65.000000\n", "NC_047559.1 4843 4845 68.421053\n", "NC_047559.1 4887 4889 70.000000\n", "NC_047559.1 4909 4911 50.000000\n", "NC_047559.1 7129 7131 77.777778\n", "NC_047559.1 7814 7816 100.000000\n", "NC_047559.1 7850 7852 100.000000\n", "NC_047559.1 7867 7869 90.000000\n", "NC_047559.1 7885 7887 81.818182\n", "\n", "==> zr3644_7_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth <==\n", "NC_047559.1 4270 4272 50.000000\n", "NC_047559.1 4835 4837 50.000000\n", "NC_047559.1 4887 4889 55.172414\n", "NC_047559.1 5605 5607 54.545455\n", "NC_047559.1 5613 5615 54.545455\n", "NC_047559.1 7129 7131 50.000000\n", "NC_047559.1 7490 7492 90.000000\n", "NC_047559.1 7671 7673 95.238095\n", "NC_047559.1 7814 7816 90.909091\n", "NC_047559.1 7850 7852 93.333333\n", "\n", "==> zr3644_8_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth <==\n", "NC_047559.1 4397 4399 60.000000\n", "NC_047559.1 4835 4837 63.888889\n", "NC_047559.1 4843 4845 58.064516\n", "NC_047559.1 4887 4889 73.333333\n", "NC_047559.1 4909 4911 55.555556\n", "NC_047559.1 5605 5607 50.000000\n", "NC_047559.1 5613 5615 66.666667\n", "NC_047559.1 7129 7131 80.000000\n", "NC_047559.1 7490 7492 63.636364\n", "NC_047559.1 7671 7673 100.000000\n", "\n", "==> zr3644_9_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth <==\n", "NC_047559.1 4073 4075 57.142857\n", "NC_047559.1 4791 4793 68.181818\n", "NC_047559.1 4835 4837 95.238095\n", "NC_047559.1 4843 4845 90.476190\n", "NC_047559.1 4887 4889 87.500000\n", "NC_047559.1 5605 5607 50.000000\n", "NC_047559.1 5613 5615 66.666667\n", "NC_047559.1 7129 7131 54.545455\n", "NC_047559.1 7490 7492 58.823529\n", "NC_047559.1 7814 7816 100.000000\n", "\n", "==> zr3644_union-averages_5x.bedgraph-Meth <==\n", "NC_047559.1 1571 1573 58.333332999999996\n", "NC_047559.1 2087 2089 60.0\n", "NC_047559.1 2267 2269 100.0\n", "NC_047559.1 2291 2293 87.5\n", "NC_047559.1 4073 4075 52.14285699999999\n", "NC_047559.1 4791 4793 53.95369170833333\n", "NC_047559.1 4835 4837 71.80917783333332\n", "NC_047559.1 4843 4845 73.73931504166667\n", "NC_047559.1 4887 4889 70.38324817391306\n", "NC_047559.1 4909 4911 50.605249\n" ] } ], "source": [ "!head *-Meth" ] }, { "cell_type": "code", "execution_count": 24, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ " 743737 zr3644_10_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth\n", " 756315 zr3644_11_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth\n", " 637993 zr3644_12_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth\n", " 740056 zr3644_13_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth\n", " 677853 zr3644_14_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth\n", " 830917 zr3644_15_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth\n", " 693543 zr3644_16_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth\n", " 734773 zr3644_17_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth\n", " 707271 zr3644_18_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth\n", " 685738 zr3644_19_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth\n", " 619143 zr3644_1_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth\n", " 723787 zr3644_20_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth\n", " 719026 zr3644_21_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth\n", " 675299 zr3644_22_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth\n", " 601988 zr3644_23_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth\n", " 714637 zr3644_24_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth\n", " 738283 zr3644_2_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth\n", " 610260 zr3644_3_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth\n", " 687146 zr3644_4_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth\n", " 661854 zr3644_5_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth\n", " 724356 zr3644_6_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth\n", " 865371 zr3644_7_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth\n", " 649827 zr3644_8_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth\n", " 676714 zr3644_9_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth\n", " 989453 zr3644_union-averages_5x.bedgraph-Meth\n", " 17865340 total\n" ] } ], "source": [ "!wc -l *-Meth" ] }, { "cell_type": "code", "execution_count": 28, "metadata": { "collapsed": false }, "outputs": [], "source": [ "#Get line counts for each fine\n", "# Remove 10th line (total entries)\n", "#Ensure output is tab-delimited\n", "#Save output\n", "!wc -l *-Meth \\\n", "| sed '26,$ d' \\\n", "| awk '{print $1\"\\t\"$2}' \\\n", "> zr3644_5x-Meth-counts.txt" ] }, { "cell_type": "code", "execution_count": 29, "metadata": { "collapsed": false, "scrolled": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "743737\tzr3644_10_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth\r\n", "756315\tzr3644_11_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth\r\n", "637993\tzr3644_12_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth\r\n", "740056\tzr3644_13_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth\r\n", "677853\tzr3644_14_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth\r\n", "830917\tzr3644_15_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth\r\n", "693543\tzr3644_16_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth\r\n", "734773\tzr3644_17_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth\r\n", "707271\tzr3644_18_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth\r\n", "685738\tzr3644_19_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth\r\n" ] } ], "source": [ "!head zr3644_5x-Meth-counts.txt" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "### 5b. Sparsely methylated loci" ] }, { "cell_type": "code", "execution_count": 30, "metadata": { "collapsed": true }, "outputs": [], "source": [ "%%bash\n", "for f in zr3644*5x.bedgraph\n", "do\n", " awk '{if ($4 < 50) { print $1, $2, $3, $4}}' ${f} \\\n", " | awk '{if ($4 > 10) { print $1, $2, $3, $4 }}' \\\n", " > ${f}-sparseMeth\n", "done" ] }, { "cell_type": "code", "execution_count": 31, "metadata": { "collapsed": true }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "==> zr3644_10_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth <==\n", "NC_001276.1 4384 4386 15.555556\n", "NC_001276.1 4396 4398 17.073171\n", "NC_001276.1 4402 4404 12.820513\n", "NC_001276.1 4444 4446 15.151515\n", "NC_001276.1 4446 4448 13.333333\n", "NC_001276.1 4488 4490 11.764706\n", "NC_047559.1 4397 4399 16.666667\n", "NC_047559.1 4909 4911 28.571429\n", "NC_047559.1 5500 5502 20.000000\n", "NC_047559.1 7129 7131 44.444444\n", "\n", "==> zr3644_11_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth <==\n", "NC_001276.1 4557 4559 10.526316\n", "NC_001276.1 4573 4575 11.111111\n", "NC_001276.1 6462 6464 11.627907\n", "NC_047559.1 4791 4793 38.461538\n", "NC_047559.1 4835 4837 48.148148\n", "NC_047559.1 4909 4911 33.333333\n", "NC_047559.1 5605 5607 30.000000\n", "NC_047559.1 5613 5615 22.222222\n", "NC_047559.1 7716 7718 33.333333\n", "NC_047559.1 8171 8173 44.444444\n", "\n", "==> zr3644_12_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth <==\n", "NC_001276.1 4485 4487 12.500000\n", "NC_047559.1 5500 5502 28.571429\n", "NC_047559.1 7129 7131 45.833333\n", "NC_047559.1 7490 7492 38.888889\n", "NC_047559.1 8295 8297 20.000000\n", "NC_047559.1 8308 8310 33.333333\n", "NC_047559.1 8310 8312 16.666667\n", "NC_047559.1 8346 8348 33.333333\n", "NC_047559.1 8376 8378 16.666667\n", "NC_047559.1 8414 8416 16.666667\n", "\n", "==> zr3644_13_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth <==\n", "NC_047559.1 4397 4399 28.571429\n", "NC_047559.1 4887 4889 45.454545\n", "NC_047559.1 5605 5607 40.000000\n", "NC_047559.1 7716 7718 25.000000\n", "NC_047559.1 8556 8558 42.857143\n", "NC_047559.1 9122 9124 25.000000\n", "NC_047559.1 9140 9142 25.000000\n", "NC_047559.1 9159 9161 31.250000\n", "NC_047559.1 9237 9239 14.285714\n", "NC_047559.1 9240 9242 12.500000\n", "\n", "==> zr3644_14_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth <==\n", "NC_001276.1 6522 6524 10.256410\n", "NC_047559.1 5605 5607 20.000000\n", "NC_047559.1 5613 5615 40.000000\n", "NC_047559.1 9603 9605 20.000000\n", "NC_047559.1 10457 10459 14.285714\n", "NC_047559.1 23360 23362 12.500000\n", "NC_047559.1 23610 23612 41.666667\n", "NC_047559.1 31135 31137 33.333333\n", "NC_047559.1 33595 33597 14.285714\n", "NC_047559.1 41242 41244 11.111111\n", "\n", "==> zr3644_15_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth <==\n", "NC_047559.1 2809 2811 40.000000\n", "NC_047559.1 4397 4399 14.285714\n", "NC_047559.1 5500 5502 14.285714\n", "NC_047559.1 5999 6001 40.000000\n", "NC_047559.1 8979 8981 15.384615\n", "NC_047559.1 9122 9124 44.117647\n", "NC_047559.1 9140 9142 28.571429\n", "NC_047559.1 9159 9161 20.588235\n", "NC_047559.1 9774 9776 12.765957\n", "NC_047559.1 9781 9783 15.909091\n", "\n", "==> zr3644_16_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth <==\n", "NC_001276.1 4557 4559 10.344828\n", "NC_047559.1 8970 8972 40.000000\n", "NC_047559.1 8979 8981 40.000000\n", "NC_047559.1 9122 9124 26.666667\n", "NC_047559.1 9140 9142 37.500000\n", "NC_047559.1 9159 9161 12.500000\n", "NC_047559.1 19097 19099 12.500000\n", "NC_047559.1 20363 20365 11.111111\n", "NC_047559.1 23610 23612 38.461538\n", "NC_047559.1 24251 24253 33.333333\n", "\n", "==> zr3644_17_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth <==\n", "NC_001276.1 4715 4717 10.256410\n", "NC_001276.1 6566 6568 12.820513\n", "NC_047559.1 4073 4075 20.000000\n", "NC_047559.1 4909 4911 46.666667\n", "NC_047559.1 5316 5318 20.000000\n", "NC_047559.1 5500 5502 36.363636\n", "NC_047559.1 5605 5607 47.058824\n", "NC_047559.1 7129 7131 42.105263\n", "NC_047559.1 18064 18066 14.285714\n", "NC_047559.1 18078 18080 14.285714\n", "\n", "==> zr3644_18_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth <==\n", "NC_001276.1 6181 6183 10.344828\n", "NC_001276.1 6270 6272 11.111111\n", "NC_047559.1 4791 4793 40.000000\n", "NC_047559.1 4887 4889 47.619048\n", "NC_047559.1 5316 5318 20.000000\n", "NC_047559.1 5605 5607 42.857143\n", "NC_047559.1 5613 5615 40.000000\n", "NC_047559.1 7716 7718 20.000000\n", "NC_047559.1 8346 8348 25.000000\n", "NC_047559.1 8376 8378 40.000000\n", "\n", "==> zr3644_19_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth <==\n", "NC_001276.1 6505 6507 10.714286\n", "NC_001276.1 6524 6526 11.538462\n", "NC_001276.1 6563 6565 16.666667\n", "NC_001276.1 6635 6637 10.344828\n", "NC_047559.1 4791 4793 35.897436\n", "NC_047559.1 8346 8348 14.285714\n", "NC_047559.1 8449 8451 33.333333\n", "NC_047559.1 9122 9124 16.666667\n", "NC_047559.1 9140 9142 14.285714\n", "NC_047559.1 9237 9239 25.000000\n", "\n", "==> zr3644_1_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth <==\n", "NC_047559.1 4887 4889 40.000000\n", "NC_047559.1 9140 9142 40.000000\n", "NC_047559.1 9159 9161 14.285714\n", "NC_047559.1 9240 9242 22.222222\n", "NC_047559.1 15162 15164 11.111111\n", "NC_047559.1 23360 23362 33.333333\n", "NC_047559.1 23610 23612 37.500000\n", "NC_047559.1 26509 26511 40.000000\n", "NC_047559.1 26561 26563 14.285714\n", "NC_047559.1 26591 26593 16.666667\n", "\n", "==> zr3644_20_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth <==\n", "NC_001276.1 4384 4386 10.606061\n", "NC_047559.1 4791 4793 28.787879\n", "NC_047559.1 4835 4837 45.454545\n", "NC_047559.1 4887 4889 42.105263\n", "NC_047559.1 4909 4911 35.714286\n", "NC_047559.1 5613 5615 33.333333\n", "NC_047559.1 7716 7718 37.500000\n", "NC_047559.1 8251 8253 40.000000\n", "NC_047559.1 8266 8268 42.857143\n", "NC_047559.1 8346 8348 40.000000\n", "\n", "==> zr3644_21_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth <==\n", "NC_001276.1 6462 6464 11.428571\n", "NC_001276.1 6480 6482 12.903226\n", "NC_001276.1 6505 6507 12.500000\n", "NC_001276.1 6793 6795 12.871287\n", "NC_047559.1 4397 4399 40.000000\n", "NC_047559.1 7716 7718 33.333333\n", "NC_047559.1 7979 7981 20.000000\n", "NC_047559.1 7990 7992 40.000000\n", "NC_047559.1 8236 8238 33.333333\n", "NC_047559.1 8251 8253 42.857143\n", "\n", "==> zr3644_22_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth <==\n", "NC_047559.1 5500 5502 20.000000\n", "NC_047559.1 5613 5615 40.000000\n", "NC_047559.1 9122 9124 20.000000\n", "NC_047559.1 9140 9142 18.181818\n", "NC_047559.1 9159 9161 11.111111\n", "NC_047559.1 9237 9239 28.571429\n", "NC_047559.1 9795 9797 13.043478\n", "NC_047559.1 9803 9805 11.428571\n", "NC_047559.1 11080 11082 20.000000\n", "NC_047559.1 21729 21731 16.666667\n", "\n", "==> zr3644_23_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth <==\n", "NC_001276.1 4384 4386 14.705882\n", "NC_001276.1 4396 4398 13.793103\n", "NC_001276.1 4402 4404 14.814815\n", "NC_001276.1 4446 4448 18.181818\n", "NC_001276.1 6097 6099 12.121212\n", "NC_001276.1 6563 6565 18.750000\n", "NC_001276.1 6566 6568 18.750000\n", "NC_047559.1 4791 4793 37.142857\n", "NC_047559.1 4909 4911 44.444444\n", "NC_047559.1 5605 5607 40.000000\n", "\n", "==> zr3644_24_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth <==\n", "NC_001276.1 4720 4722 10.185185\n", "NC_047559.1 4791 4793 35.000000\n", "NC_047559.1 7716 7718 28.571429\n", "NC_047559.1 8346 8348 12.500000\n", "NC_047559.1 8556 8558 33.333333\n", "NC_047559.1 8979 8981 20.000000\n", "NC_047559.1 9122 9124 30.769231\n", "NC_047559.1 9140 9142 23.076923\n", "NC_047559.1 9159 9161 11.764706\n", "NC_047559.1 9237 9239 20.000000\n", "\n", "==> zr3644_2_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth <==\n", "NC_001276.1 4427 4429 12.195122\n", "NC_001276.1 6566 6568 14.285714\n", "NC_001276.1 6793 6795 10.144928\n", "NC_001276.1 6807 6809 10.884354\n", "NC_047559.1 5291 5293 20.000000\n", "NC_047559.1 5605 5607 41.666667\n", "NC_047559.1 5613 5615 45.454545\n", "NC_047559.1 7716 7718 42.857143\n", "NC_047559.1 7959 7961 42.857143\n", "NC_047559.1 7979 7981 40.000000\n", "\n", "==> zr3644_3_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth <==\n", "NC_001276.1 4485 4487 18.181818\n", "NC_001276.1 4488 4490 18.181818\n", "NC_001276.1 4557 4559 20.000000\n", "NC_001276.1 6462 6464 12.000000\n", "NC_001276.1 6474 6476 10.204082\n", "NC_001276.1 6563 6565 15.384615\n", "NC_047559.1 8266 8268 16.666667\n", "NC_047559.1 8295 8297 40.000000\n", "NC_047559.1 8346 8348 40.000000\n", "NC_047559.1 8376 8378 42.857143\n", "\n", "==> zr3644_4_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth <==\n", "NC_001276.1 4427 4429 14.285714\n", "NC_047559.1 4791 4793 32.000000\n", "NC_047559.1 4835 4837 41.176471\n", "NC_047559.1 4843 4845 40.000000\n", "NC_047559.1 5500 5502 44.444444\n", "NC_047559.1 5605 5607 42.857143\n", "NC_047559.1 5613 5615 42.857143\n", "NC_047559.1 8970 8972 20.000000\n", "NC_047559.1 8979 8981 20.000000\n", "NC_047559.1 9140 9142 42.105263\n", "\n", "==> zr3644_5_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth <==\n", "NC_001276.1 4444 4446 15.384615\n", "NC_001276.1 4446 4448 16.000000\n", "NC_001276.1 4485 4487 15.384615\n", "NC_047559.1 4270 4272 40.000000\n", "NC_047559.1 4397 4399 33.333333\n", "NC_047559.1 5605 5607 20.000000\n", "NC_047559.1 5613 5615 40.000000\n", "NC_047559.1 7716 7718 16.666667\n", "NC_047559.1 8556 8558 25.000000\n", "NC_047559.1 9122 9124 43.750000\n", "\n", "==> zr3644_6_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth <==\n", "NC_001276.1 4384 4386 10.526316\n", "NC_001276.1 6462 6464 10.416667\n", "NC_001276.1 6480 6482 11.764706\n", "NC_047559.1 4791 4793 46.153846\n", "NC_047559.1 5500 5502 37.500000\n", "NC_047559.1 7490 7492 44.444444\n", "NC_047559.1 7671 7673 42.857143\n", "NC_047559.1 8236 8238 40.000000\n", "NC_047559.1 8970 8972 30.434783\n", "NC_047559.1 8979 8981 35.000000\n", "\n", "==> zr3644_7_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth <==\n", "NC_001276.1 4402 4404 12.307692\n", "NC_001276.1 6793 6795 10.400000\n", "NC_001276.1 6798 6800 10.505837\n", "NC_047559.1 1571 1573 33.333333\n", "NC_047559.1 4397 4399 40.000000\n", "NC_047559.1 4791 4793 32.432432\n", "NC_047559.1 4843 4845 46.428571\n", "NC_047559.1 4909 4911 28.571429\n", "NC_047559.1 5291 5293 33.333333\n", "NC_047559.1 5316 5318 44.444444\n", "\n", "==> zr3644_8_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth <==\n", "NC_001276.1 6462 6464 10.256410\n", "NC_001276.1 6474 6476 13.157895\n", "NC_001276.1 6480 6482 11.428571\n", "NC_001276.1 6524 6526 10.344828\n", "NC_047559.1 4791 4793 45.238095\n", "NC_047559.1 7716 7718 22.222222\n", "NC_047559.1 8171 8173 20.000000\n", "NC_047559.1 8217 8219 16.666667\n", "NC_047559.1 8254 8256 33.333333\n", "NC_047559.1 8346 8348 33.333333\n", "\n", "==> zr3644_9_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth <==\n", "NC_001276.1 6563 6565 11.111111\n", "NC_001276.1 6807 6809 10.179641\n", "NC_047559.1 7716 7718 33.333333\n", "NC_047559.1 8970 8972 16.666667\n", "NC_047559.1 9122 9124 20.000000\n", "NC_047559.1 9774 9776 19.230769\n", "NC_047559.1 9781 9783 29.166667\n", "NC_047559.1 9787 9789 26.086957\n", "NC_047559.1 9795 9797 26.315789\n", "NC_047559.1 9803 9805 18.750000\n", "\n", "==> zr3644_union-averages_5x.bedgraph-sparseMeth <==\n", "NC_047559.1 2809 2811 40.0\n", "NC_047559.1 4270 4272 47.5\n", "NC_047559.1 4397 4399 24.40476191666667\n", "NC_047559.1 5291 5293 26.6666665\n", "NC_047559.1 5316 5318 33.5978835\n", "NC_047559.1 5500 5502 32.201889\n", "NC_047559.1 5605 5607 39.7580055625\n", "NC_047559.1 5613 5615 47.762515307692304\n", "NC_047559.1 5999 6001 40.0\n", "NC_047559.1 6439 6441 20.0\n" ] } ], "source": [ "!head *-sparseMeth" ] }, { "cell_type": "code", "execution_count": 32, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ " 528855 zr3644_10_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth\n", " 558684 zr3644_11_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth\n", " 495856 zr3644_12_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth\n", " 567817 zr3644_13_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth\n", " 354184 zr3644_14_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth\n", " 571945 zr3644_15_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth\n", " 501880 zr3644_16_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth\n", " 487599 zr3644_17_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth\n", " 531718 zr3644_18_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth\n", " 506442 zr3644_19_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth\n", " 523037 zr3644_1_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth\n", " 549976 zr3644_20_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth\n", " 548000 zr3644_21_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth\n", " 498782 zr3644_22_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth\n", " 447553 zr3644_23_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth\n", " 525877 zr3644_24_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth\n", " 486067 zr3644_2_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth\n", " 457255 zr3644_3_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth\n", " 516004 zr3644_4_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth\n", " 500164 zr3644_5_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth\n", " 539459 zr3644_6_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth\n", " 657007 zr3644_7_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth\n", " 473775 zr3644_8_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth\n", " 501924 zr3644_9_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth\n", " 848655 zr3644_union-averages_5x.bedgraph-sparseMeth\n", " 13178515 total\n" ] } ], "source": [ "!wc -l *-sparseMeth" ] }, { "cell_type": "code", "execution_count": 33, "metadata": { "collapsed": false }, "outputs": [], "source": [ "#Get line counts for each fine\n", "# Remove 10th line (total entries)\n", "#Ensure output is tab-delimited\n", "#Save output\n", "!wc -l *-sparseMeth \\\n", "| sed '26,$ d' \\\n", "| awk '{print $1\"\\t\"$2}' \\\n", "> zr3644_5x-sparseMeth-counts.txt" ] }, { "cell_type": "code", "execution_count": 34, "metadata": { "collapsed": false, "scrolled": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "528855\tzr3644_10_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth\r\n", "558684\tzr3644_11_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth\r\n", "495856\tzr3644_12_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth\r\n", "567817\tzr3644_13_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth\r\n", "354184\tzr3644_14_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth\r\n", "571945\tzr3644_15_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth\r\n", "501880\tzr3644_16_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth\r\n", "487599\tzr3644_17_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth\r\n", "531718\tzr3644_18_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth\r\n", "506442\tzr3644_19_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth\r\n" ] } ], "source": [ "!head zr3644_5x-sparseMeth-counts.txt" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "### 5c. Unmethylated loci" ] }, { "cell_type": "code", "execution_count": 35, "metadata": { "collapsed": true }, "outputs": [], "source": [ "%%bash\n", "for f in zr3644*5x.bedgraph\n", "do\n", " awk '{if ($4 <= 10) { print $1, $2, $3, $4 }}' ${f} \\\n", " > ${f}-unMeth\n", "done" ] }, { "cell_type": "code", "execution_count": 36, "metadata": { "collapsed": true }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "==> zr3644_10_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth <==\n", "NC_001276.1 34 36 3.092784\n", "NC_001276.1 123 125 0.851064\n", "NC_001276.1 305 307 3.314917\n", "NC_001276.1 433 435 1.986755\n", "NC_001276.1 457 459 1.538462\n", "NC_001276.1 482 484 0.638978\n", "NC_001276.1 609 611 1.479290\n", "NC_001276.1 781 783 1.457726\n", "NC_001276.1 826 828 1.346801\n", "NC_001276.1 951 953 5.645161\n", "\n", "==> zr3644_11_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth <==\n", "NC_001276.1 34 36 1.162791\n", "NC_001276.1 123 125 0.425532\n", "NC_001276.1 305 307 1.081081\n", "NC_001276.1 433 435 1.167315\n", "NC_001276.1 457 459 2.158273\n", "NC_001276.1 482 484 2.076125\n", "NC_001276.1 609 611 1.543210\n", "NC_001276.1 781 783 1.298701\n", "NC_001276.1 826 828 2.205882\n", "NC_001276.1 951 953 1.785714\n", "\n", "==> zr3644_12_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth <==\n", "NC_001276.1 34 36 3.061224\n", "NC_001276.1 123 125 0.826446\n", "NC_001276.1 305 307 3.225806\n", "NC_001276.1 433 435 1.133144\n", "NC_001276.1 457 459 0.529101\n", "NC_001276.1 482 484 1.749271\n", "NC_001276.1 609 611 2.425876\n", "NC_001276.1 781 783 1.941748\n", "NC_001276.1 826 828 2.298851\n", "NC_001276.1 951 953 3.720930\n", "\n", "==> zr3644_13_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth <==\n", "NC_001276.1 34 36 3.401361\n", "NC_001276.1 123 125 0.755668\n", "NC_001276.1 305 307 1.955307\n", "NC_001276.1 433 435 0.569260\n", "NC_001276.1 457 459 0.172117\n", "NC_001276.1 482 484 0.743494\n", "NC_001276.1 609 611 1.589825\n", "NC_001276.1 781 783 1.379310\n", "NC_001276.1 826 828 0.200401\n", "NC_001276.1 951 953 1.794872\n", "\n", "==> zr3644_14_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth <==\n", "NC_001276.1 34 36 3.614458\n", "NC_001276.1 123 125 1.562500\n", "NC_001276.1 305 307 6.578947\n", "NC_001276.1 433 435 0.881057\n", "NC_001276.1 457 459 1.195219\n", "NC_001276.1 482 484 0.000000\n", "NC_001276.1 609 611 1.742160\n", "NC_001276.1 781 783 2.238806\n", "NC_001276.1 826 828 0.823045\n", "NC_001276.1 951 953 3.763441\n", "\n", "==> zr3644_15_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth <==\n", "NC_001276.1 34 36 2.659574\n", "NC_001276.1 123 125 0.821355\n", "NC_001276.1 305 307 2.739726\n", "NC_001276.1 433 435 1.798561\n", "NC_001276.1 457 459 1.487603\n", "NC_001276.1 482 484 1.587302\n", "NC_001276.1 609 611 1.497006\n", "NC_001276.1 781 783 1.121795\n", "NC_001276.1 826 828 2.161100\n", "NC_001276.1 951 953 2.594340\n", "\n", "==> zr3644_16_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth <==\n", "NC_001276.1 34 36 4.375000\n", "NC_001276.1 123 125 0.493827\n", "NC_001276.1 305 307 1.973684\n", "NC_001276.1 433 435 1.212121\n", "NC_001276.1 457 459 0.560748\n", "NC_001276.1 482 484 1.242236\n", "NC_001276.1 609 611 1.876173\n", "NC_001276.1 781 783 1.740812\n", "NC_001276.1 826 828 0.883002\n", "NC_001276.1 951 953 2.191781\n", "\n", "==> zr3644_17_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth <==\n", "NC_001276.1 34 36 4.347826\n", "NC_001276.1 123 125 1.100917\n", "NC_001276.1 305 307 2.403846\n", "NC_001276.1 433 435 1.658375\n", "NC_001276.1 457 459 1.397516\n", "NC_001276.1 482 484 1.490066\n", "NC_001276.1 609 611 1.923077\n", "NC_001276.1 781 783 3.153153\n", "NC_001276.1 826 828 2.117264\n", "NC_001276.1 951 953 4.883721\n", "\n", "==> zr3644_18_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth <==\n", "NC_001276.1 34 36 4.054054\n", "NC_001276.1 123 125 0.819672\n", "NC_001276.1 305 307 2.427184\n", "NC_001276.1 433 435 1.292407\n", "NC_001276.1 457 459 0.765697\n", "NC_001276.1 482 484 1.162791\n", "NC_001276.1 609 611 2.737752\n", "NC_001276.1 781 783 2.489019\n", "NC_001276.1 826 828 1.036269\n", "NC_001276.1 951 953 1.769912\n", "\n", "==> zr3644_19_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth <==\n", "NC_001276.1 34 36 3.603604\n", "NC_001276.1 123 125 0.387597\n", "NC_001276.1 305 307 1.777778\n", "NC_001276.1 433 435 1.273885\n", "NC_001276.1 457 459 1.479290\n", "NC_001276.1 482 484 1.428571\n", "NC_001276.1 609 611 1.734104\n", "NC_001276.1 781 783 2.747253\n", "NC_001276.1 826 828 1.796407\n", "NC_001276.1 951 953 3.652968\n", "\n", "==> zr3644_1_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth <==\n", "NC_001276.1 34 36 2.343750\n", "NC_001276.1 123 125 2.006689\n", "NC_001276.1 305 307 2.525253\n", "NC_001276.1 433 435 0.284900\n", "NC_001276.1 457 459 1.033592\n", "NC_001276.1 482 484 1.149425\n", "NC_001276.1 609 611 0.997506\n", "NC_001276.1 781 783 2.843602\n", "NC_001276.1 826 828 0.831025\n", "NC_001276.1 951 953 4.435484\n", "\n", "==> zr3644_20_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth <==\n", "NC_001276.1 34 36 3.468208\n", "NC_001276.1 123 125 0.956938\n", "NC_001276.1 305 307 3.669725\n", "NC_001276.1 433 435 1.541426\n", "NC_001276.1 457 459 0.910747\n", "NC_001276.1 482 484 0.589391\n", "NC_001276.1 609 611 2.101576\n", "NC_001276.1 781 783 1.325758\n", "NC_001276.1 826 828 1.237113\n", "NC_001276.1 951 953 3.299492\n", "\n", "==> zr3644_21_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth <==\n", "NC_001276.1 34 36 2.083333\n", "NC_001276.1 123 125 0.000000\n", "NC_001276.1 305 307 4.848485\n", "NC_001276.1 433 435 0.743494\n", "NC_001276.1 457 459 1.754386\n", "NC_001276.1 482 484 0.729927\n", "NC_001276.1 609 611 2.654867\n", "NC_001276.1 781 783 1.597444\n", "NC_001276.1 826 828 1.379310\n", "NC_001276.1 951 953 1.369863\n", "\n", "==> zr3644_22_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth <==\n", "NC_001276.1 34 36 2.453988\n", "NC_001276.1 123 125 0.512821\n", "NC_001276.1 305 307 3.846154\n", "NC_001276.1 433 435 0.649351\n", "NC_001276.1 457 459 0.769231\n", "NC_001276.1 482 484 1.568627\n", "NC_001276.1 609 611 1.883562\n", "NC_001276.1 781 783 1.449275\n", "NC_001276.1 826 828 1.131222\n", "NC_001276.1 951 953 2.046036\n", "\n", "==> zr3644_23_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth <==\n", "NC_001276.1 34 36 6.250000\n", "NC_001276.1 123 125 1.115242\n", "NC_001276.1 305 307 3.255814\n", "NC_001276.1 433 435 1.562500\n", "NC_001276.1 457 459 0.857143\n", "NC_001276.1 482 484 1.269841\n", "NC_001276.1 609 611 2.777778\n", "NC_001276.1 781 783 3.651685\n", "NC_001276.1 826 828 1.010101\n", "NC_001276.1 951 953 3.652968\n", "\n", "==> zr3644_24_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth <==\n", "NC_001276.1 34 36 5.479452\n", "NC_001276.1 123 125 1.020408\n", "NC_001276.1 305 307 5.166052\n", "NC_001276.1 433 435 1.834862\n", "NC_001276.1 457 459 0.643777\n", "NC_001276.1 482 484 1.207729\n", "NC_001276.1 609 611 2.024291\n", "NC_001276.1 781 783 1.840491\n", "NC_001276.1 826 828 1.345291\n", "NC_001276.1 951 953 2.640264\n", "\n", "==> zr3644_2_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth <==\n", "NC_001276.1 34 36 9.615385\n", "NC_001276.1 123 125 0.378788\n", "NC_001276.1 305 307 2.843602\n", "NC_001276.1 433 435 1.277955\n", "NC_001276.1 457 459 1.159420\n", "NC_001276.1 482 484 2.395210\n", "NC_001276.1 609 611 1.837270\n", "NC_001276.1 781 783 1.608579\n", "NC_001276.1 826 828 1.333333\n", "NC_001276.1 951 953 4.545455\n", "\n", "==> zr3644_3_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth <==\n", "NC_001276.1 34 36 6.862745\n", "NC_001276.1 123 125 0.396825\n", "NC_001276.1 305 307 5.687204\n", "NC_001276.1 433 435 2.473498\n", "NC_001276.1 457 459 0.619195\n", "NC_001276.1 482 484 1.612903\n", "NC_001276.1 609 611 3.954802\n", "NC_001276.1 781 783 2.295082\n", "NC_001276.1 826 828 1.503759\n", "NC_001276.1 951 953 3.571429\n", "\n", "==> zr3644_4_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth <==\n", "NC_001276.1 34 36 5.217391\n", "NC_001276.1 123 125 1.689189\n", "NC_001276.1 305 307 2.517986\n", "NC_001276.1 433 435 0.997506\n", "NC_001276.1 457 459 2.142857\n", "NC_001276.1 482 484 1.790281\n", "NC_001276.1 609 611 0.938967\n", "NC_001276.1 781 783 1.909308\n", "NC_001276.1 826 828 0.879765\n", "NC_001276.1 951 953 1.798561\n", "\n", "==> zr3644_5_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth <==\n", "NC_001276.1 34 36 1.785714\n", "NC_001276.1 123 125 0.727273\n", "NC_001276.1 305 307 1.621622\n", "NC_001276.1 433 435 1.506024\n", "NC_001276.1 457 459 1.983003\n", "NC_001276.1 482 484 1.436782\n", "NC_001276.1 609 611 3.359173\n", "NC_001276.1 781 783 2.209945\n", "NC_001276.1 826 828 1.577287\n", "NC_001276.1 951 953 2.834008\n", "\n", "==> zr3644_6_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth <==\n", "NC_001276.1 34 36 2.150538\n", "NC_001276.1 123 125 1.176471\n", "NC_001276.1 305 307 1.630435\n", "NC_001276.1 433 435 1.683502\n", "NC_001276.1 457 459 1.238390\n", "NC_001276.1 482 484 0.911854\n", "NC_001276.1 609 611 3.200000\n", "NC_001276.1 781 783 2.727273\n", "NC_001276.1 826 828 1.048951\n", "NC_001276.1 951 953 5.000000\n", "\n", "==> zr3644_7_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth <==\n", "NC_001276.1 34 36 3.389831\n", "NC_001276.1 123 125 0.845666\n", "NC_001276.1 305 307 4.450262\n", "NC_001276.1 433 435 1.680672\n", "NC_001276.1 457 459 1.374046\n", "NC_001276.1 482 484 1.176471\n", "NC_001276.1 609 611 2.352941\n", "NC_001276.1 781 783 3.744150\n", "NC_001276.1 826 828 2.229846\n", "NC_001276.1 951 953 4.453441\n", "\n", "==> zr3644_8_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth <==\n", "NC_001276.1 34 36 2.380952\n", "NC_001276.1 123 125 1.287554\n", "NC_001276.1 305 307 4.040404\n", "NC_001276.1 433 435 2.135231\n", "NC_001276.1 457 459 2.317881\n", "NC_001276.1 482 484 1.736111\n", "NC_001276.1 609 611 2.866242\n", "NC_001276.1 781 783 3.508772\n", "NC_001276.1 826 828 1.886792\n", "NC_001276.1 951 953 4.950495\n", "\n", "==> zr3644_9_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth <==\n", "NC_001276.1 34 36 5.303030\n", "NC_001276.1 123 125 1.315789\n", "NC_001276.1 305 307 3.873239\n", "NC_001276.1 433 435 2.153110\n", "NC_001276.1 457 459 1.830664\n", "NC_001276.1 482 484 0.477327\n", "NC_001276.1 609 611 1.716738\n", "NC_001276.1 781 783 1.434426\n", "NC_001276.1 826 828 1.162791\n", "NC_001276.1 951 953 3.603604\n", "\n", "==> zr3644_union-averages_5x.bedgraph-unMeth <==\n", "NC_001276.1 34 36 3.8398747083333338\n", "NC_001276.1 123 125 0.894759625\n", "NC_001276.1 305 307 3.2272713749999995\n", "NC_001276.1 433 435 1.3957046250000003\n", "NC_001276.1 457 459 1.2465982500000001\n", "NC_001276.1 482 484 1.2571130416666667\n", "NC_001276.1 609 611 2.1339244166666664\n", "NC_001276.1 781 783 2.1547547083333334\n", "NC_001276.1 826 828 1.3927336666666665\n", "NC_001276.1 951 953 3.3334975000000004\n" ] } ], "source": [ "!head *-unMeth" ] }, { "cell_type": "code", "execution_count": 37, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ " 5209767 zr3644_10_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth\n", " 5479027 zr3644_11_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth\n", " 5010195 zr3644_12_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth\n", " 5373555 zr3644_13_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth\n", " 4141333 zr3644_14_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth\n", " 5572667 zr3644_15_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth\n", " 4938951 zr3644_16_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth\n", " 5375811 zr3644_17_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth\n", " 5109927 zr3644_18_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth\n", " 5089706 zr3644_19_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth\n", " 4999645 zr3644_1_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth\n", " 5323583 zr3644_20_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth\n", " 5230773 zr3644_21_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth\n", " 4917890 zr3644_22_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth\n", " 4386784 zr3644_23_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth\n", " 5226081 zr3644_24_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth\n", " 5468369 zr3644_2_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth\n", " 4428948 zr3644_3_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth\n", " 5153467 zr3644_4_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth\n", " 4808449 zr3644_5_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth\n", " 5314172 zr3644_6_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth\n", " 6535083 zr3644_7_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth\n", " 4627939 zr3644_8_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth\n", " 4706202 zr3644_9_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth\n", " 8659212 zr3644_union-averages_5x.bedgraph-unMeth\n", " 131087536 total\n" ] } ], "source": [ "!wc -l *-unMeth" ] }, { "cell_type": "code", "execution_count": 38, "metadata": { "collapsed": false }, "outputs": [], "source": [ "#Get line counts for each fine\n", "# Remove 10th line (total entries)\n", "#Ensure output is tab-delimited\n", "#Save output\n", "!wc -l *-unMeth \\\n", "| sed '26,$ d' \\\n", "| awk '{print $1\"\\t\"$2}' \\\n", "> zr3644_5x-unMeth-counts.txt" ] }, { "cell_type": "code", "execution_count": 39, "metadata": { "collapsed": false, "scrolled": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "5209767\tzr3644_10_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth\r\n", "5479027\tzr3644_11_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth\r\n", "5010195\tzr3644_12_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth\r\n", "5373555\tzr3644_13_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth\r\n", "4141333\tzr3644_14_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth\r\n", "5572667\tzr3644_15_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth\r\n", "4938951\tzr3644_16_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth\r\n", "5375811\tzr3644_17_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth\r\n", "5109927\tzr3644_18_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth\r\n", "5089706\tzr3644_19_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth\r\n" ] } ], "source": [ "!head zr3644_5x-unMeth-counts.txt" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "## 6. Characterize genomic location of CpGs" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "I will identify overlaps between CpG loci (methylated, sparsely methylated, unmethylated) and various genome feature tracks:\n", "\n", "- gene\n", "- exon UTR\n", "- CDS\n", "- intron\n", "- upstream flanks\n", "- downstream flanks\n", "- intergenic regions\n", "- lncRNA\n", "- transposable elements\n", "\n", "Since the exon track = exon UTR + CDS, and mRNA = exon + intron, I will not need to use those tracks separately." ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "### 6a. Create BEDfiles" ] }, { "cell_type": "code", "execution_count": 40, "metadata": { "collapsed": false, "scrolled": true }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "zr3644_10_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth\n", "zr3644_10_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth\n", "zr3644_10_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth\n", "zr3644_11_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth\n", "zr3644_11_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth\n", "zr3644_11_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth\n", "zr3644_12_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth\n", "zr3644_12_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth\n", "zr3644_12_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth\n", "zr3644_13_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth\n", "zr3644_13_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth\n", "zr3644_13_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth\n", "zr3644_14_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth\n", "zr3644_14_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth\n", "zr3644_14_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth\n", "zr3644_15_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth\n", "zr3644_15_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth\n", "zr3644_15_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth\n", "zr3644_16_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth\n", "zr3644_16_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth\n", "zr3644_16_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth\n", "zr3644_17_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth\n", "zr3644_17_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth\n", "zr3644_17_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth\n", "zr3644_18_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth\n", "zr3644_18_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth\n", "zr3644_18_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth\n", "zr3644_19_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth\n", "zr3644_19_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth\n", "zr3644_19_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth\n", "zr3644_1_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth\n", "zr3644_1_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth\n", "zr3644_1_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth\n", "zr3644_20_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth\n", "zr3644_20_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth\n", "zr3644_20_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth\n", "zr3644_21_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth\n", "zr3644_21_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth\n", "zr3644_21_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth\n", "zr3644_22_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth\n", "zr3644_22_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth\n", "zr3644_22_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth\n", "zr3644_23_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth\n", "zr3644_23_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth\n", "zr3644_23_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth\n", "zr3644_24_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth\n", "zr3644_24_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth\n", "zr3644_24_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth\n", "zr3644_2_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth\n", "zr3644_2_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth\n", "zr3644_2_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth\n", "zr3644_3_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth\n", "zr3644_3_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth\n", "zr3644_3_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth\n", "zr3644_4_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth\n", "zr3644_4_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth\n", "zr3644_4_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth\n", "zr3644_5_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth\n", "zr3644_5_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth\n", "zr3644_5_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth\n", "zr3644_6_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth\n", "zr3644_6_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth\n", "zr3644_6_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth\n", "zr3644_7_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth\n", "zr3644_7_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth\n", "zr3644_7_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth\n", "zr3644_8_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth\n", "zr3644_8_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth\n", "zr3644_8_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth\n", "zr3644_9_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth\n", "zr3644_9_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth\n", "zr3644_9_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth\n", "zr3644_union-averages_5x.bedgraph-Meth\n", "zr3644_union-averages_5x.bedgraph-sparseMeth\n", "zr3644_union-averages_5x.bedgraph-unMeth\n", " 75\n" ] } ], "source": [ "#25 file types (24 samples + 1 union), 3 files per type (Meth, sparseMeth, unMeth) = 75 total\n", "!find zr3644*5x.bedgraph-*\n", "!find zr3644*5x.bedgraph-* | wc -l" ] }, { "cell_type": "code", "execution_count": 41, "metadata": { "collapsed": false, "scrolled": true }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ " 743737 zr3644_10_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed\n", " 528855 zr3644_10_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed\n", " 5209767 zr3644_10_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed\n", " 756315 zr3644_11_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed\n", " 558684 zr3644_11_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed\n", " 5479027 zr3644_11_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed\n", " 637993 zr3644_12_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed\n", " 495856 zr3644_12_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed\n", " 5010195 zr3644_12_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed\n", " 740056 zr3644_13_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed\n", " 567817 zr3644_13_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed\n", " 5373555 zr3644_13_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed\n", " 677853 zr3644_14_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed\n", " 354184 zr3644_14_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed\n", " 4141333 zr3644_14_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed\n", " 830917 zr3644_15_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed\n", " 571945 zr3644_15_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed\n", " 5572667 zr3644_15_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed\n", " 693543 zr3644_16_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed\n", " 501880 zr3644_16_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed\n", " 4938951 zr3644_16_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed\n", " 734773 zr3644_17_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed\n", " 487599 zr3644_17_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed\n", " 5375811 zr3644_17_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed\n", " 707271 zr3644_18_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed\n", " 531718 zr3644_18_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed\n", " 5109927 zr3644_18_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed\n", " 685738 zr3644_19_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed\n", " 506442 zr3644_19_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed\n", " 5089706 zr3644_19_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed\n", " 619143 zr3644_1_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed\n", " 523037 zr3644_1_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed\n", " 4999645 zr3644_1_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed\n", " 723787 zr3644_20_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed\n", " 549976 zr3644_20_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed\n", " 5323583 zr3644_20_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed\n", " 719026 zr3644_21_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed\n", " 548000 zr3644_21_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed\n", " 5230773 zr3644_21_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed\n", " 675299 zr3644_22_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed\n", " 498782 zr3644_22_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed\n", " 4917890 zr3644_22_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed\n", " 601988 zr3644_23_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed\n", " 447553 zr3644_23_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed\n", " 4386784 zr3644_23_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed\n", " 714637 zr3644_24_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed\n", " 525877 zr3644_24_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed\n", " 5226081 zr3644_24_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed\n", " 738283 zr3644_2_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed\n", " 486067 zr3644_2_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed\n", " 5468369 zr3644_2_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed\n", " 610260 zr3644_3_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed\n", " 457255 zr3644_3_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed\n", " 4428948 zr3644_3_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed\n", " 687146 zr3644_4_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed\n", " 516004 zr3644_4_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed\n", " 5153467 zr3644_4_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed\n", " 661854 zr3644_5_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed\n", " 500164 zr3644_5_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed\n", " 4808449 zr3644_5_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed\n", " 724356 zr3644_6_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed\n", " 539459 zr3644_6_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed\n", " 5314172 zr3644_6_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed\n", " 865371 zr3644_7_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed\n", " 657007 zr3644_7_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed\n", " 6535083 zr3644_7_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed\n", " 649827 zr3644_8_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed\n", " 473775 zr3644_8_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed\n", " 4627939 zr3644_8_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed\n", " 676714 zr3644_9_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed\n", " 501924 zr3644_9_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed\n", " 4706202 zr3644_9_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed\n", " 989453 zr3644_union-averages_5x.bedgraph-Meth.bed\n", " 848655 zr3644_union-averages_5x.bedgraph-sparseMeth.bed\n", " 8659212 zr3644_union-averages_5x.bedgraph-unMeth.bed\n" ] } ], "source": [ "%%bash\n", "\n", "for f in zr3644*5x.bedgraph-*\n", "do\n", " awk '{print $1\"\\t\"$2\"\\t\"$3}' ${f} > ${f}.bed\n", " wc -l ${f}.bed\n", "done" ] }, { "cell_type": "code", "execution_count": 6, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "NC_001276.1\t34\t36\r\n", "NC_001276.1\t123\t125\r\n", "NC_001276.1\t305\t307\r\n", "NC_001276.1\t433\t435\r\n", "NC_001276.1\t457\t459\r\n", "NC_001276.1\t482\t484\r\n", "NC_001276.1\t609\t611\r\n", "NC_001276.1\t781\t783\r\n", "NC_001276.1\t826\t828\r\n", "NC_001276.1\t951\t953\r\n" ] } ], "source": [ "#Convert 1x bedgraph (DSS CpG background) to BEDfile. \n", "#Remove header\n", "#Save output: Will intersect with genes to get information important for annotation\n", "!awk '{print $1\"\\t\"$2\"\\t\"$3}' union_1x.bedgraph \\\n", "| tail -n+2 \\\n", "> union_1x.bedgraph.bed\n", "!head union_1x.bedgraph.bed" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "### 6b. Gene" ] }, { "cell_type": "code", "execution_count": 42, "metadata": { "collapsed": false }, "outputs": [], "source": [ "%%bash\n", "for f in *bed\n", "do\n", " /Users/Shared/bioinformatics/bedtools2/bin/intersectBed \\\n", " -u \\\n", " -a ${f} \\\n", " -b /Volumes/web-1/halfshell/genomic-databank/cgigas_uk_roslin_v1_gene.gff \\\n", " > ${f}-Gene\n", "done" ] }, { "cell_type": "code", "execution_count": 43, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "==> zr3644_10_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-Gene <==\n", "NC_047559.1\t356335\t356337\n", "NC_047559.1\t356436\t356438\n", "NC_047559.1\t356685\t356687\n", "NC_047559.1\t357799\t357801\n", "NC_047559.1\t357900\t357902\n", "NC_047559.1\t357955\t357957\n", "NC_047559.1\t358313\t358315\n", "NC_047559.1\t362609\t362611\n", "NC_047559.1\t416078\t416080\n", "NC_047559.1\t416920\t416922\n", "\n", "==> zr3644_10_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-Gene <==\n", "NC_047559.1\t10270\t10272\n", "NC_047559.1\t10292\t10294\n", "NC_047559.1\t10358\t10360\n", "NC_047559.1\t18257\t18259\n", "NC_047559.1\t61081\t61083\n", "NC_047559.1\t62770\t62772\n", "NC_047559.1\t68070\t68072\n", "NC_047559.1\t72245\t72247\n", "NC_047559.1\t81263\t81265\n", "NC_047559.1\t100249\t100251\n", "\n", "==> zr3644_10_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-Gene <==\n", "NC_047559.1\t10314\t10316\n", "NC_047559.1\t10845\t10847\n", "NC_047559.1\t10859\t10861\n", "NC_047559.1\t10899\t10901\n", "NC_047559.1\t10920\t10922\n", "NC_047559.1\t10950\t10952\n", "NC_047559.1\t11000\t11002\n", "NC_047559.1\t11026\t11028\n", "NC_047559.1\t14214\t14216\n", "NC_047559.1\t14232\t14234\n", "\n", "==> zr3644_11_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-Gene <==\n", "NC_047559.1\t139898\t139900\n", "NC_047559.1\t139912\t139914\n", "NC_047559.1\t139926\t139928\n", "NC_047559.1\t139945\t139947\n", "NC_047559.1\t139954\t139956\n", "NC_047559.1\t139972\t139974\n", "NC_047559.1\t139998\t140000\n", "NC_047559.1\t140007\t140009\n", "NC_047559.1\t140046\t140048\n", "NC_047559.1\t154324\t154326\n", "\n", "==> zr3644_11_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-Gene <==\n", "NC_047559.1\t17973\t17975\n", "NC_047559.1\t61203\t61205\n", "NC_047559.1\t62770\t62772\n", "NC_047559.1\t68070\t68072\n", "NC_047559.1\t100154\t100156\n", "NC_047559.1\t122491\t122493\n", "NC_047559.1\t139389\t139391\n", "NC_047559.1\t140083\t140085\n", "NC_047559.1\t140131\t140133\n", "NC_047559.1\t140139\t140141\n", "\n", "==> zr3644_11_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-Gene <==\n", "NC_047559.1\t10155\t10157\n", "NC_047559.1\t10215\t10217\n", "NC_047559.1\t10270\t10272\n", "NC_047559.1\t10292\t10294\n", "NC_047559.1\t10314\t10316\n", "NC_047559.1\t10358\t10360\n", "NC_047559.1\t10402\t10404\n", "NC_047559.1\t10413\t10415\n", "NC_047559.1\t10457\t10459\n", "NC_047559.1\t10479\t10481\n", "\n", "==> zr3644_12_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-Gene <==\n", "NC_047559.1\t424694\t424696\n", "NC_047559.1\t424941\t424943\n", "NC_047559.1\t425000\t425002\n", "NC_047559.1\t425018\t425020\n", "NC_047559.1\t425106\t425108\n", "NC_047559.1\t425124\t425126\n", "NC_047559.1\t425144\t425146\n", "NC_047559.1\t425159\t425161\n", "NC_047559.1\t425403\t425405\n", "NC_047559.1\t425491\t425493\n", "\n", "==> zr3644_12_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-Gene <==\n", "NC_047559.1\t10358\t10360\n", "NC_047559.1\t10772\t10774\n", "NC_047559.1\t19113\t19115\n", "NC_047559.1\t61081\t61083\n", "NC_047559.1\t62770\t62772\n", "NC_047559.1\t100180\t100182\n", "NC_047559.1\t140934\t140936\n", "NC_047559.1\t140963\t140965\n", "NC_047559.1\t140978\t140980\n", "NC_047559.1\t140984\t140986\n", "\n", "==> zr3644_12_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-Gene <==\n", "NC_047559.1\t10215\t10217\n", "NC_047559.1\t10270\t10272\n", "NC_047559.1\t10292\t10294\n", "NC_047559.1\t10314\t10316\n", "NC_047559.1\t10402\t10404\n", "NC_047559.1\t10413\t10415\n", "NC_047559.1\t10457\t10459\n", "NC_047559.1\t10479\t10481\n", "NC_047559.1\t10501\t10503\n", "NC_047559.1\t10545\t10547\n", "\n", "==> zr3644_13_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-Gene <==\n", "NC_047559.1\t139998\t140000\n", "NC_047559.1\t140007\t140009\n", "NC_047559.1\t338430\t338432\n", "NC_047559.1\t356335\t356337\n", "NC_047559.1\t356748\t356750\n", "NC_047559.1\t357501\t357503\n", "NC_047559.1\t357519\t357521\n", "NC_047559.1\t357784\t357786\n", "NC_047559.1\t357799\t357801\n", "NC_047559.1\t357900\t357902\n", "\n", "==> zr3644_13_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-Gene <==\n", "NC_047559.1\t10270\t10272\n", "NC_047559.1\t62770\t62772\n", "NC_047559.1\t68070\t68072\n", "NC_047559.1\t100180\t100182\n", "NC_047559.1\t100276\t100278\n", "NC_047559.1\t111728\t111730\n", "NC_047559.1\t113151\t113153\n", "NC_047559.1\t139438\t139440\n", "NC_047559.1\t140046\t140048\n", "NC_047559.1\t140295\t140297\n", "\n", "==> zr3644_13_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-Gene <==\n", "NC_047559.1\t10292\t10294\n", "NC_047559.1\t10314\t10316\n", "NC_047559.1\t10358\t10360\n", "NC_047559.1\t10479\t10481\n", "NC_047559.1\t10501\t10503\n", "NC_047559.1\t10545\t10547\n", "NC_047559.1\t10547\t10549\n", "NC_047559.1\t10567\t10569\n", "NC_047559.1\t10772\t10774\n", "NC_047559.1\t10845\t10847\n", "\n", "==> zr3644_14_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-Gene <==\n", "NC_047559.1\t62770\t62772\n", "NC_047559.1\t68070\t68072\n", "NC_047559.1\t164604\t164606\n", "NC_047559.1\t164626\t164628\n", "NC_047559.1\t164628\t164630\n", "NC_047559.1\t164642\t164644\n", "NC_047559.1\t164647\t164649\n", "NC_047559.1\t164662\t164664\n", "NC_047559.1\t375360\t375362\n", "NC_047559.1\t377621\t377623\n", "\n", "==> zr3644_14_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-Gene <==\n", "NC_047559.1\t10457\t10459\n", "NC_047559.1\t60430\t60432\n", "NC_047559.1\t61081\t61083\n", "NC_047559.1\t61203\t61205\n", "NC_047559.1\t116738\t116740\n", "NC_047559.1\t139430\t139432\n", "NC_047559.1\t144144\t144146\n", "NC_047559.1\t161452\t161454\n", "NC_047559.1\t161468\t161470\n", "NC_047559.1\t161483\t161485\n", "\n", "==> zr3644_14_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-Gene <==\n", "NC_047559.1\t10270\t10272\n", "NC_047559.1\t10292\t10294\n", "NC_047559.1\t10314\t10316\n", "NC_047559.1\t10358\t10360\n", "NC_047559.1\t10391\t10393\n", "NC_047559.1\t10402\t10404\n", "NC_047559.1\t10413\t10415\n", "NC_047559.1\t10479\t10481\n", "NC_047559.1\t10545\t10547\n", "NC_047559.1\t10612\t10614\n", "\n", "==> zr3644_15_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-Gene <==\n", "NC_047559.1\t99190\t99192\n", "NC_047559.1\t139972\t139974\n", "NC_047559.1\t139998\t140000\n", "NC_047559.1\t140007\t140009\n", "NC_047559.1\t140046\t140048\n", "NC_047559.1\t140539\t140541\n", "NC_047559.1\t140557\t140559\n", "NC_047559.1\t140589\t140591\n", "NC_047559.1\t140640\t140642\n", "NC_047559.1\t356335\t356337\n", "\n", "==> zr3644_15_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-Gene <==\n", "NC_047559.1\t10215\t10217\n", "NC_047559.1\t19113\t19115\n", "NC_047559.1\t80380\t80382\n", "NC_047559.1\t82007\t82009\n", "NC_047559.1\t83035\t83037\n", "NC_047559.1\t84068\t84070\n", "NC_047559.1\t100440\t100442\n", "NC_047559.1\t100964\t100966\n", "NC_047559.1\t107909\t107911\n", "NC_047559.1\t111760\t111762\n", "\n", "==> zr3644_15_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-Gene <==\n", "NC_047559.1\t10155\t10157\n", "NC_047559.1\t10270\t10272\n", "NC_047559.1\t10292\t10294\n", "NC_047559.1\t10314\t10316\n", "NC_047559.1\t10358\t10360\n", "NC_047559.1\t10391\t10393\n", "NC_047559.1\t10457\t10459\n", "NC_047559.1\t10479\t10481\n", "NC_047559.1\t10501\t10503\n", "NC_047559.1\t10545\t10547\n", "\n", "==> zr3644_16_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-Gene <==\n", "NC_047559.1\t338777\t338779\n", "NC_047559.1\t338819\t338821\n", "NC_047559.1\t338862\t338864\n", "NC_047559.1\t338883\t338885\n", "NC_047559.1\t339095\t339097\n", "NC_047559.1\t341533\t341535\n", "NC_047559.1\t341535\t341537\n", "NC_047559.1\t342302\t342304\n", "NC_047559.1\t342692\t342694\n", "NC_047559.1\t342699\t342701\n", "\n", "==> zr3644_16_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-Gene <==\n", "NC_047559.1\t19097\t19099\n", "NC_047559.1\t62770\t62772\n", "NC_047559.1\t80469\t80471\n", "NC_047559.1\t139430\t139432\n", "NC_047559.1\t139438\t139440\n", "NC_047559.1\t141298\t141300\n", "NC_047559.1\t154324\t154326\n", "NC_047559.1\t169393\t169395\n", "NC_047559.1\t169415\t169417\n", "NC_047559.1\t169433\t169435\n", "\n", "==> zr3644_16_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-Gene <==\n", "NC_047559.1\t10845\t10847\n", "NC_047559.1\t10859\t10861\n", "NC_047559.1\t10899\t10901\n", "NC_047559.1\t10920\t10922\n", "NC_047559.1\t10950\t10952\n", "NC_047559.1\t14214\t14216\n", "NC_047559.1\t14232\t14234\n", "NC_047559.1\t14243\t14245\n", "NC_047559.1\t14259\t14261\n", "NC_047559.1\t14319\t14321\n", "\n", "==> zr3644_17_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-Gene <==\n", "NC_047559.1\t337326\t337328\n", "NC_047559.1\t340780\t340782\n", "NC_047559.1\t340787\t340789\n", "NC_047559.1\t340813\t340815\n", "NC_047559.1\t359671\t359673\n", "NC_047559.1\t359678\t359680\n", "NC_047559.1\t359701\t359703\n", "NC_047559.1\t360322\t360324\n", "NC_047559.1\t360361\t360363\n", "NC_047559.1\t360443\t360445\n", "\n", "==> zr3644_17_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-Gene <==\n", "NC_047559.1\t18064\t18066\n", "NC_047559.1\t18078\t18080\n", "NC_047559.1\t18332\t18334\n", "NC_047559.1\t68070\t68072\n", "NC_047559.1\t68140\t68142\n", "NC_047559.1\t82158\t82160\n", "NC_047559.1\t85405\t85407\n", "NC_047559.1\t115136\t115138\n", "NC_047559.1\t125225\t125227\n", "NC_047559.1\t139334\t139336\n", "\n", "==> zr3644_17_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-Gene <==\n", "NC_047559.1\t10380\t10382\n", "NC_047559.1\t10391\t10393\n", "NC_047559.1\t10402\t10404\n", "NC_047559.1\t10413\t10415\n", "NC_047559.1\t10457\t10459\n", "NC_047559.1\t10479\t10481\n", "NC_047559.1\t10501\t10503\n", "NC_047559.1\t10545\t10547\n", "NC_047559.1\t10547\t10549\n", "NC_047559.1\t10567\t10569\n", "\n", "==> zr3644_18_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-Gene <==\n", "NC_047559.1\t139972\t139974\n", "NC_047559.1\t139998\t140000\n", "NC_047559.1\t140007\t140009\n", "NC_047559.1\t140046\t140048\n", "NC_047559.1\t140520\t140522\n", "NC_047559.1\t140539\t140541\n", "NC_047559.1\t140557\t140559\n", "NC_047559.1\t140589\t140591\n", "NC_047559.1\t140640\t140642\n", "NC_047559.1\t140894\t140896\n", "\n", "==> zr3644_18_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-Gene <==\n", "NC_047559.1\t10358\t10360\n", "NC_047559.1\t11026\t11028\n", "NC_047559.1\t18152\t18154\n", "NC_047559.1\t80380\t80382\n", "NC_047559.1\t82357\t82359\n", "NC_047559.1\t82835\t82837\n", "NC_047559.1\t100154\t100156\n", "NC_047559.1\t100276\t100278\n", "NC_047559.1\t100305\t100307\n", "NC_047559.1\t113151\t113153\n", "\n", "==> zr3644_18_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-Gene <==\n", "NC_047559.1\t10270\t10272\n", "NC_047559.1\t10292\t10294\n", "NC_047559.1\t10314\t10316\n", "NC_047559.1\t10380\t10382\n", "NC_047559.1\t10391\t10393\n", "NC_047559.1\t10402\t10404\n", "NC_047559.1\t10413\t10415\n", "NC_047559.1\t10457\t10459\n", "NC_047559.1\t10479\t10481\n", "NC_047559.1\t10501\t10503\n", "\n", "==> zr3644_19_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-Gene <==\n", "NC_047559.1\t140894\t140896\n", "NC_047559.1\t338777\t338779\n", "NC_047559.1\t338862\t338864\n", "NC_047559.1\t338883\t338885\n", "NC_047559.1\t340874\t340876\n", "NC_047559.1\t356335\t356337\n", "NC_047559.1\t356430\t356432\n", "NC_047559.1\t356436\t356438\n", "NC_047559.1\t356699\t356701\n", "NC_047559.1\t357362\t357364\n", "\n", "==> zr3644_19_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-Gene <==\n", "NC_047559.1\t11080\t11082\n", "NC_047559.1\t14862\t14864\n", "NC_047559.1\t62770\t62772\n", "NC_047559.1\t83475\t83477\n", "NC_047559.1\t100305\t100307\n", "NC_047559.1\t139297\t139299\n", "NC_047559.1\t139334\t139336\n", "NC_047559.1\t139389\t139391\n", "NC_047559.1\t139396\t139398\n", "NC_047559.1\t139438\t139440\n", "\n", "==> zr3644_19_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-Gene <==\n", "NC_047559.1\t10155\t10157\n", "NC_047559.1\t10215\t10217\n", "NC_047559.1\t10270\t10272\n", "NC_047559.1\t10292\t10294\n", "NC_047559.1\t10314\t10316\n", "NC_047559.1\t10358\t10360\n", "NC_047559.1\t10402\t10404\n", "NC_047559.1\t10413\t10415\n", "NC_047559.1\t10457\t10459\n", "NC_047559.1\t10479\t10481\n", "\n", "==> zr3644_1_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-Gene <==\n", "NC_047559.1\t68070\t68072\n", "NC_047559.1\t338430\t338432\n", "NC_047559.1\t338444\t338446\n", "NC_047559.1\t356378\t356380\n", "NC_047559.1\t356395\t356397\n", "NC_047559.1\t356910\t356912\n", "NC_047559.1\t356933\t356935\n", "NC_047559.1\t358586\t358588\n", "NC_047559.1\t359671\t359673\n", "NC_047559.1\t377838\t377840\n", "\n", "==> zr3644_1_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-Gene <==\n", "NC_047559.1\t15162\t15164\n", "NC_047559.1\t62935\t62937\n", "NC_047559.1\t68140\t68142\n", "NC_047559.1\t84364\t84366\n", "NC_047559.1\t104216\t104218\n", "NC_047559.1\t117736\t117738\n", "NC_047559.1\t119924\t119926\n", "NC_047559.1\t159869\t159871\n", "NC_047559.1\t159881\t159883\n", "NC_047559.1\t160416\t160418\n", "\n", "==> zr3644_1_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-Gene <==\n", "NC_047559.1\t10215\t10217\n", "NC_047559.1\t10270\t10272\n", "NC_047559.1\t10292\t10294\n", "NC_047559.1\t10314\t10316\n", "NC_047559.1\t10358\t10360\n", "NC_047559.1\t10380\t10382\n", "NC_047559.1\t10391\t10393\n", "NC_047559.1\t10402\t10404\n", "NC_047559.1\t10413\t10415\n", "NC_047559.1\t10457\t10459\n", "\n", "==> zr3644_20_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-Gene <==\n", "NC_047559.1\t60313\t60315\n", "NC_047559.1\t60371\t60373\n", "NC_047559.1\t360361\t360363\n", "NC_047559.1\t416920\t416922\n", "NC_047559.1\t424894\t424896\n", "NC_047559.1\t424941\t424943\n", "NC_047559.1\t425000\t425002\n", "NC_047559.1\t425018\t425020\n", "NC_047559.1\t425106\t425108\n", "NC_047559.1\t425124\t425126\n", "\n", "==> zr3644_20_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-Gene <==\n", "NC_047559.1\t14243\t14245\n", "NC_047559.1\t62770\t62772\n", "NC_047559.1\t82012\t82014\n", "NC_047559.1\t82761\t82763\n", "NC_047559.1\t100249\t100251\n", "NC_047559.1\t100319\t100321\n", "NC_047559.1\t122867\t122869\n", "NC_047559.1\t153777\t153779\n", "NC_047559.1\t153830\t153832\n", "NC_047559.1\t153840\t153842\n", "\n", "==> zr3644_20_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-Gene <==\n", "NC_047559.1\t10270\t10272\n", "NC_047559.1\t10292\t10294\n", "NC_047559.1\t10314\t10316\n", "NC_047559.1\t10358\t10360\n", "NC_047559.1\t10402\t10404\n", "NC_047559.1\t10413\t10415\n", "NC_047559.1\t10479\t10481\n", "NC_047559.1\t10501\t10503\n", "NC_047559.1\t10545\t10547\n", "NC_047559.1\t10547\t10549\n", "\n", "==> zr3644_21_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-Gene <==\n", "NC_047559.1\t356699\t356701\n", "NC_047559.1\t356910\t356912\n", "NC_047559.1\t356933\t356935\n", "NC_047559.1\t357501\t357503\n", "NC_047559.1\t357519\t357521\n", "NC_047559.1\t357751\t357753\n", "NC_047559.1\t357784\t357786\n", "NC_047559.1\t357799\t357801\n", "NC_047559.1\t419514\t419516\n", "NC_047559.1\t424694\t424696\n", "\n", "==> zr3644_21_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-Gene <==\n", "NC_047559.1\t61081\t61083\n", "NC_047559.1\t104628\t104630\n", "NC_047559.1\t140377\t140379\n", "NC_047559.1\t140381\t140383\n", "NC_047559.1\t140557\t140559\n", "NC_047559.1\t140589\t140591\n", "NC_047559.1\t140894\t140896\n", "NC_047559.1\t140934\t140936\n", "NC_047559.1\t140963\t140965\n", "NC_047559.1\t140978\t140980\n", "\n", "==> zr3644_21_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-Gene <==\n", "NC_047559.1\t10155\t10157\n", "NC_047559.1\t10215\t10217\n", "NC_047559.1\t10270\t10272\n", "NC_047559.1\t10292\t10294\n", "NC_047559.1\t10314\t10316\n", "NC_047559.1\t10479\t10481\n", "NC_047559.1\t10501\t10503\n", "NC_047559.1\t10545\t10547\n", "NC_047559.1\t10547\t10549\n", "NC_047559.1\t10645\t10647\n", "\n", "==> zr3644_22_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-Gene <==\n", "NC_047559.1\t154324\t154326\n", "NC_047559.1\t356395\t356397\n", "NC_047559.1\t356430\t356432\n", "NC_047559.1\t356436\t356438\n", "NC_047559.1\t356532\t356534\n", "NC_047559.1\t358313\t358315\n", "NC_047559.1\t358375\t358377\n", "NC_047559.1\t358503\t358505\n", "NC_047559.1\t358527\t358529\n", "NC_047559.1\t360322\t360324\n", "\n", "==> zr3644_22_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-Gene <==\n", "NC_047559.1\t11080\t11082\n", "NC_047559.1\t62770\t62772\n", "NC_047559.1\t68070\t68072\n", "NC_047559.1\t100276\t100278\n", "NC_047559.1\t100319\t100321\n", "NC_047559.1\t123636\t123638\n", "NC_047559.1\t139334\t139336\n", "NC_047559.1\t139430\t139432\n", "NC_047559.1\t139438\t139440\n", "NC_047559.1\t139443\t139445\n", "\n", "==> zr3644_22_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-Gene <==\n", "NC_047559.1\t10155\t10157\n", "NC_047559.1\t10270\t10272\n", "NC_047559.1\t10292\t10294\n", "NC_047559.1\t10314\t10316\n", "NC_047559.1\t10457\t10459\n", "NC_047559.1\t10479\t10481\n", "NC_047559.1\t10501\t10503\n", "NC_047559.1\t10545\t10547\n", "NC_047559.1\t10547\t10549\n", "NC_047559.1\t10567\t10569\n", "\n", "==> zr3644_23_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-Gene <==\n", "NC_047559.1\t356335\t356337\n", "NC_047559.1\t356378\t356380\n", "NC_047559.1\t356395\t356397\n", "NC_047559.1\t356430\t356432\n", "NC_047559.1\t356436\t356438\n", "NC_047559.1\t356832\t356834\n", "NC_047559.1\t356933\t356935\n", "NC_047559.1\t357784\t357786\n", "NC_047559.1\t357799\t357801\n", "NC_047559.1\t358313\t358315\n", "\n", "==> zr3644_23_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-Gene <==\n", "NC_047559.1\t62770\t62772\n", "NC_047559.1\t104267\t104269\n", "NC_047559.1\t123167\t123169\n", "NC_047559.1\t123489\t123491\n", "NC_047559.1\t140083\t140085\n", "NC_047559.1\t140377\t140379\n", "NC_047559.1\t140381\t140383\n", "NC_047559.1\t140424\t140426\n", "NC_047559.1\t140589\t140591\n", "NC_047559.1\t140934\t140936\n", "\n", "==> zr3644_23_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-Gene <==\n", "NC_047559.1\t10270\t10272\n", "NC_047559.1\t10292\t10294\n", "NC_047559.1\t10314\t10316\n", "NC_047559.1\t10358\t10360\n", "NC_047559.1\t10545\t10547\n", "NC_047559.1\t10547\t10549\n", "NC_047559.1\t10567\t10569\n", "NC_047559.1\t10592\t10594\n", "NC_047559.1\t10772\t10774\n", "NC_047559.1\t10845\t10847\n", "\n", "==> zr3644_24_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-Gene <==\n", "NC_047559.1\t356436\t356438\n", "NC_047559.1\t356910\t356912\n", "NC_047559.1\t356933\t356935\n", "NC_047559.1\t357751\t357753\n", "NC_047559.1\t357784\t357786\n", "NC_047559.1\t357799\t357801\n", "NC_047559.1\t357900\t357902\n", "NC_047559.1\t357947\t357949\n", "NC_047559.1\t357955\t357957\n", "NC_047559.1\t358035\t358037\n", "\n", "==> zr3644_24_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-Gene <==\n", "NC_047559.1\t10547\t10549\n", "NC_047559.1\t10645\t10647\n", "NC_047559.1\t10950\t10952\n", "NC_047559.1\t19105\t19107\n", "NC_047559.1\t19113\t19115\n", "NC_047559.1\t19119\t19121\n", "NC_047559.1\t62770\t62772\n", "NC_047559.1\t100751\t100753\n", "NC_047559.1\t113151\t113153\n", "NC_047559.1\t120270\t120272\n", "\n", "==> zr3644_24_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-Gene <==\n", "NC_047559.1\t10270\t10272\n", "NC_047559.1\t10292\t10294\n", "NC_047559.1\t10314\t10316\n", "NC_047559.1\t10545\t10547\n", "NC_047559.1\t10567\t10569\n", "NC_047559.1\t10592\t10594\n", "NC_047559.1\t10612\t10614\n", "NC_047559.1\t10667\t10669\n", "NC_047559.1\t10772\t10774\n", "NC_047559.1\t10845\t10847\n", "\n", "==> zr3644_2_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-Gene <==\n", "NC_047559.1\t61081\t61083\n", "NC_047559.1\t359678\t359680\n", "NC_047559.1\t360322\t360324\n", "NC_047559.1\t360361\t360363\n", "NC_047559.1\t424894\t424896\n", "NC_047559.1\t424941\t424943\n", "NC_047559.1\t425000\t425002\n", "NC_047559.1\t425018\t425020\n", "NC_047559.1\t425065\t425067\n", "NC_047559.1\t425106\t425108\n", "\n", "==> zr3644_2_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-Gene <==\n", "NC_047559.1\t10501\t10503\n", "NC_047559.1\t10772\t10774\n", "NC_047559.1\t10845\t10847\n", "NC_047559.1\t11026\t11028\n", "NC_047559.1\t19113\t19115\n", "NC_047559.1\t62770\t62772\n", "NC_047559.1\t68070\t68072\n", "NC_047559.1\t100180\t100182\n", "NC_047559.1\t104439\t104441\n", "NC_047559.1\t104697\t104699\n", "\n", "==> zr3644_2_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-Gene <==\n", "NC_047559.1\t10155\t10157\n", "NC_047559.1\t10270\t10272\n", "NC_047559.1\t10292\t10294\n", "NC_047559.1\t10314\t10316\n", "NC_047559.1\t10358\t10360\n", "NC_047559.1\t10380\t10382\n", "NC_047559.1\t10391\t10393\n", "NC_047559.1\t10402\t10404\n", "NC_047559.1\t10413\t10415\n", "NC_047559.1\t10457\t10459\n", "\n", "==> zr3644_3_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-Gene <==\n", "NC_047559.1\t338430\t338432\n", "NC_047559.1\t338444\t338446\n", "NC_047559.1\t338617\t338619\n", "NC_047559.1\t340912\t340914\n", "NC_047559.1\t340923\t340925\n", "NC_047559.1\t341839\t341841\n", "NC_047559.1\t342246\t342248\n", "NC_047559.1\t342250\t342252\n", "NC_047559.1\t356933\t356935\n", "NC_047559.1\t357519\t357521\n", "\n", "==> zr3644_3_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-Gene <==\n", "NC_047559.1\t62770\t62772\n", "NC_047559.1\t100276\t100278\n", "NC_047559.1\t115724\t115726\n", "NC_047559.1\t154507\t154509\n", "NC_047559.1\t169652\t169654\n", "NC_047559.1\t227983\t227985\n", "NC_047559.1\t337565\t337567\n", "NC_047559.1\t337616\t337618\n", "NC_047559.1\t337624\t337626\n", "NC_047559.1\t337639\t337641\n", "\n", "==> zr3644_3_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-Gene <==\n", "NC_047559.1\t10215\t10217\n", "NC_047559.1\t10270\t10272\n", "NC_047559.1\t10292\t10294\n", "NC_047559.1\t10314\t10316\n", "NC_047559.1\t10358\t10360\n", "NC_047559.1\t10402\t10404\n", "NC_047559.1\t10413\t10415\n", "NC_047559.1\t10457\t10459\n", "NC_047559.1\t10479\t10481\n", "NC_047559.1\t10501\t10503\n", "\n", "==> zr3644_4_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-Gene <==\n", "NC_047559.1\t154507\t154509\n", "NC_047559.1\t356395\t356397\n", "NC_047559.1\t356436\t356438\n", "NC_047559.1\t356699\t356701\n", "NC_047559.1\t356748\t356750\n", "NC_047559.1\t356910\t356912\n", "NC_047559.1\t356933\t356935\n", "NC_047559.1\t357362\t357364\n", "NC_047559.1\t357382\t357384\n", "NC_047559.1\t357396\t357398\n", "\n", "==> zr3644_4_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-Gene <==\n", "NC_047559.1\t10479\t10481\n", "NC_047559.1\t18003\t18005\n", "NC_047559.1\t61081\t61083\n", "NC_047559.1\t61203\t61205\n", "NC_047559.1\t62770\t62772\n", "NC_047559.1\t109247\t109249\n", "NC_047559.1\t113151\t113153\n", "NC_047559.1\t139430\t139432\n", "NC_047559.1\t139438\t139440\n", "NC_047559.1\t139443\t139445\n", "\n", "==> zr3644_4_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-Gene <==\n", "NC_047559.1\t10155\t10157\n", "NC_047559.1\t10270\t10272\n", "NC_047559.1\t10292\t10294\n", "NC_047559.1\t10314\t10316\n", "NC_047559.1\t10358\t10360\n", "NC_047559.1\t10501\t10503\n", "NC_047559.1\t10545\t10547\n", "NC_047559.1\t10547\t10549\n", "NC_047559.1\t10567\t10569\n", "NC_047559.1\t10592\t10594\n", "\n", "==> zr3644_5_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-Gene <==\n", "NC_047559.1\t140539\t140541\n", "NC_047559.1\t140557\t140559\n", "NC_047559.1\t140589\t140591\n", "NC_047559.1\t140640\t140642\n", "NC_047559.1\t356335\t356337\n", "NC_047559.1\t356378\t356380\n", "NC_047559.1\t356395\t356397\n", "NC_047559.1\t356430\t356432\n", "NC_047559.1\t356436\t356438\n", "NC_047559.1\t357362\t357364\n", "\n", "==> zr3644_5_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-Gene <==\n", "NC_047559.1\t19113\t19115\n", "NC_047559.1\t61081\t61083\n", "NC_047559.1\t62770\t62772\n", "NC_047559.1\t80725\t80727\n", "NC_047559.1\t80737\t80739\n", "NC_047559.1\t139972\t139974\n", "NC_047559.1\t139998\t140000\n", "NC_047559.1\t140007\t140009\n", "NC_047559.1\t140046\t140048\n", "NC_047559.1\t140083\t140085\n", "\n", "==> zr3644_5_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-Gene <==\n", "NC_047559.1\t10155\t10157\n", "NC_047559.1\t10215\t10217\n", "NC_047559.1\t10270\t10272\n", "NC_047559.1\t10292\t10294\n", "NC_047559.1\t10314\t10316\n", "NC_047559.1\t10358\t10360\n", "NC_047559.1\t10402\t10404\n", "NC_047559.1\t10413\t10415\n", "NC_047559.1\t10457\t10459\n", "NC_047559.1\t10479\t10481\n", "\n", "==> zr3644_6_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-Gene <==\n", "NC_047559.1\t139945\t139947\n", "NC_047559.1\t139954\t139956\n", "NC_047559.1\t139972\t139974\n", "NC_047559.1\t139998\t140000\n", "NC_047559.1\t140539\t140541\n", "NC_047559.1\t140557\t140559\n", "NC_047559.1\t140589\t140591\n", "NC_047559.1\t337624\t337626\n", "NC_047559.1\t337639\t337641\n", "NC_047559.1\t341781\t341783\n", "\n", "==> zr3644_6_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-Gene <==\n", "NC_047559.1\t19097\t19099\n", "NC_047559.1\t61081\t61083\n", "NC_047559.1\t62770\t62772\n", "NC_047559.1\t68070\t68072\n", "NC_047559.1\t100154\t100156\n", "NC_047559.1\t113151\t113153\n", "NC_047559.1\t113369\t113371\n", "NC_047559.1\t140007\t140009\n", "NC_047559.1\t140046\t140048\n", "NC_047559.1\t140083\t140085\n", "\n", "==> zr3644_6_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-Gene <==\n", "NC_047559.1\t10155\t10157\n", "NC_047559.1\t10215\t10217\n", "NC_047559.1\t10270\t10272\n", "NC_047559.1\t10292\t10294\n", "NC_047559.1\t10314\t10316\n", "NC_047559.1\t10457\t10459\n", "NC_047559.1\t10479\t10481\n", "NC_047559.1\t10501\t10503\n", "NC_047559.1\t10545\t10547\n", "NC_047559.1\t10547\t10549\n", "\n", "==> zr3644_7_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-Gene <==\n", "NC_047559.1\t140589\t140591\n", "NC_047559.1\t140640\t140642\n", "NC_047559.1\t356378\t356380\n", "NC_047559.1\t356395\t356397\n", "NC_047559.1\t356430\t356432\n", "NC_047559.1\t356436\t356438\n", "NC_047559.1\t356532\t356534\n", "NC_047559.1\t356748\t356750\n", "NC_047559.1\t356910\t356912\n", "NC_047559.1\t356933\t356935\n", "\n", "==> zr3644_7_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-Gene <==\n", "NC_047559.1\t10380\t10382\n", "NC_047559.1\t19083\t19085\n", "NC_047559.1\t19097\t19099\n", "NC_047559.1\t19105\t19107\n", "NC_047559.1\t61203\t61205\n", "NC_047559.1\t62770\t62772\n", "NC_047559.1\t62935\t62937\n", "NC_047559.1\t71969\t71971\n", "NC_047559.1\t71973\t71975\n", "NC_047559.1\t71994\t71996\n", "\n", "==> zr3644_7_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-Gene <==\n", "NC_047559.1\t10155\t10157\n", "NC_047559.1\t10215\t10217\n", "NC_047559.1\t10270\t10272\n", "NC_047559.1\t10292\t10294\n", "NC_047559.1\t10314\t10316\n", "NC_047559.1\t10358\t10360\n", "NC_047559.1\t10391\t10393\n", "NC_047559.1\t10402\t10404\n", "NC_047559.1\t10413\t10415\n", "NC_047559.1\t10457\t10459\n", "\n", "==> zr3644_8_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-Gene <==\n", "NC_047559.1\t378417\t378419\n", "NC_047559.1\t378455\t378457\n", "NC_047559.1\t424894\t424896\n", "NC_047559.1\t424941\t424943\n", "NC_047559.1\t425000\t425002\n", "NC_047559.1\t425018\t425020\n", "NC_047559.1\t425106\t425108\n", "NC_047559.1\t425124\t425126\n", "NC_047559.1\t425144\t425146\n", "NC_047559.1\t425159\t425161\n", "\n", "==> zr3644_8_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-Gene <==\n", "NC_047559.1\t19097\t19099\n", "NC_047559.1\t19105\t19107\n", "NC_047559.1\t19113\t19115\n", "NC_047559.1\t19119\t19121\n", "NC_047559.1\t84487\t84489\n", "NC_047559.1\t139430\t139432\n", "NC_047559.1\t154324\t154326\n", "NC_047559.1\t154349\t154351\n", "NC_047559.1\t154507\t154509\n", "NC_047559.1\t157657\t157659\n", "\n", "==> zr3644_8_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-Gene <==\n", "NC_047559.1\t10270\t10272\n", "NC_047559.1\t10292\t10294\n", "NC_047559.1\t10314\t10316\n", "NC_047559.1\t10413\t10415\n", "NC_047559.1\t10457\t10459\n", "NC_047559.1\t10479\t10481\n", "NC_047559.1\t10501\t10503\n", "NC_047559.1\t10545\t10547\n", "NC_047559.1\t10547\t10549\n", "NC_047559.1\t10567\t10569\n", "\n", "==> zr3644_9_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-Gene <==\n", "NC_047559.1\t140520\t140522\n", "NC_047559.1\t140539\t140541\n", "NC_047559.1\t140557\t140559\n", "NC_047559.1\t140589\t140591\n", "NC_047559.1\t140640\t140642\n", "NC_047559.1\t359664\t359666\n", "NC_047559.1\t359671\t359673\n", "NC_047559.1\t359678\t359680\n", "NC_047559.1\t417944\t417946\n", "NC_047559.1\t419514\t419516\n", "\n", "==> zr3644_9_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-Gene <==\n", "NC_047559.1\t62770\t62772\n", "NC_047559.1\t68140\t68142\n", "NC_047559.1\t100154\t100156\n", "NC_047559.1\t100180\t100182\n", "NC_047559.1\t100249\t100251\n", "NC_047559.1\t100305\t100307\n", "NC_047559.1\t104313\t104315\n", "NC_047559.1\t104324\t104326\n", "NC_047559.1\t114971\t114973\n", "NC_047559.1\t115632\t115634\n", "\n", "==> zr3644_9_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-Gene <==\n", "NC_047559.1\t10391\t10393\n", "NC_047559.1\t10402\t10404\n", "NC_047559.1\t10413\t10415\n", "NC_047559.1\t10845\t10847\n", "NC_047559.1\t10859\t10861\n", "NC_047559.1\t10899\t10901\n", "NC_047559.1\t10920\t10922\n", "NC_047559.1\t10950\t10952\n", "NC_047559.1\t11000\t11002\n", "NC_047559.1\t14214\t14216\n", "\n", "==> zr3644_union-averages_5x.bedgraph-Meth.bed-Gene <==\n", "NC_047559.1\t60313\t60315\n", "NC_047559.1\t60371\t60373\n", "NC_047559.1\t139898\t139900\n", "NC_047559.1\t139912\t139914\n", "NC_047559.1\t139926\t139928\n", "NC_047559.1\t139945\t139947\n", "NC_047559.1\t139954\t139956\n", "NC_047559.1\t139972\t139974\n", "NC_047559.1\t140539\t140541\n", "NC_047559.1\t358586\t358588\n", "\n", "==> zr3644_union-averages_5x.bedgraph-sparseMeth.bed-Gene <==\n", "NC_047559.1\t60430\t60432\n", "NC_047559.1\t61081\t61083\n", "NC_047559.1\t62770\t62772\n", "NC_047559.1\t62935\t62937\n", "NC_047559.1\t68070\t68072\n", "NC_047559.1\t68140\t68142\n", "NC_047559.1\t72245\t72247\n", "NC_047559.1\t84068\t84070\n", "NC_047559.1\t100964\t100966\n", "NC_047559.1\t107909\t107911\n", "\n", "==> zr3644_union-averages_5x.bedgraph-unMeth.bed-Gene <==\n", "NC_047559.1\t10155\t10157\n", "NC_047559.1\t10215\t10217\n", "NC_047559.1\t10270\t10272\n", "NC_047559.1\t10292\t10294\n", "NC_047559.1\t10314\t10316\n", "NC_047559.1\t10358\t10360\n", "NC_047559.1\t10380\t10382\n", "NC_047559.1\t10391\t10393\n", "NC_047559.1\t10402\t10404\n", "NC_047559.1\t10413\t10415\n" ] } ], "source": [ "#Check output\n", "!head *Gene" ] }, { "cell_type": "code", "execution_count": 44, "metadata": { "collapsed": false, "scrolled": true }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ " 704609 zr3644_10_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-Gene\n", " 375370 zr3644_10_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-Gene\n", " 2973037 zr3644_10_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-Gene\n", " 715222 zr3644_11_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-Gene\n", " 396962 zr3644_11_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-Gene\n", " 3102569 zr3644_11_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-Gene\n", " 603534 zr3644_12_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-Gene\n", " 357468 zr3644_12_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-Gene\n", " 2835308 zr3644_12_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-Gene\n", " 700738 zr3644_13_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-Gene\n", " 409307 zr3644_13_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-Gene\n", " 3040647 zr3644_13_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-Gene\n", " 642967 zr3644_14_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-Gene\n", " 244579 zr3644_14_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-Gene\n", " 2399014 zr3644_14_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-Gene\n", " 785689 zr3644_15_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-Gene\n", " 406774 zr3644_15_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-Gene\n", " 3115643 zr3644_15_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-Gene\n", " 658076 zr3644_16_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-Gene\n", " 359627 zr3644_16_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-Gene\n", " 2833313 zr3644_16_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-Gene\n", " 691938 zr3644_17_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-Gene\n", " 346529 zr3644_17_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-Gene\n", " 3054945 zr3644_17_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-Gene\n", " 671264 zr3644_18_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-Gene\n", " 383245 zr3644_18_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-Gene\n", " 2923171 zr3644_18_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-Gene\n", " 650971 zr3644_19_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-Gene\n", " 365074 zr3644_19_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-Gene\n", " 2906423 zr3644_19_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-Gene\n", " 586947 zr3644_1_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-Gene\n", " 389623 zr3644_1_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-Gene\n", " 2876397 zr3644_1_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-Gene\n", " 686357 zr3644_20_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-Gene\n", " 395921 zr3644_20_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-Gene\n", " 3018215 zr3644_20_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-Gene\n", " 681643 zr3644_21_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-Gene\n", " 396186 zr3644_21_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-Gene\n", " 2972915 zr3644_21_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-Gene\n", " 641170 zr3644_22_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-Gene\n", " 359423 zr3644_22_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-Gene\n", " 2825316 zr3644_22_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-Gene\n", " 573365 zr3644_23_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-Gene\n", " 324182 zr3644_23_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-Gene\n", " 2548030 zr3644_23_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-Gene\n", " 677683 zr3644_24_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-Gene\n", " 379671 zr3644_24_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-Gene\n", " 2974613 zr3644_24_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-Gene\n", " 695138 zr3644_2_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-Gene\n", " 346679 zr3644_2_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-Gene\n", " 3099546 zr3644_2_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-Gene\n", " 579921 zr3644_3_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-Gene\n", " 329152 zr3644_3_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-Gene\n", " 2561668 zr3644_3_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-Gene\n", " 652042 zr3644_4_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-Gene\n", " 370763 zr3644_4_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-Gene\n", " 2928933 zr3644_4_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-Gene\n", " 628577 zr3644_5_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-Gene\n", " 361975 zr3644_5_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-Gene\n", " 2761837 zr3644_5_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-Gene\n", " 686722 zr3644_6_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-Gene\n", " 386635 zr3644_6_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-Gene\n", " 3018300 zr3644_6_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-Gene\n", " 814136 zr3644_7_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-Gene\n", " 463842 zr3644_7_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-Gene\n", " 3599847 zr3644_7_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-Gene\n", " 616664 zr3644_8_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-Gene\n", " 339759 zr3644_8_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-Gene\n", " 2671226 zr3644_8_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-Gene\n", " 642942 zr3644_9_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-Gene\n", " 359723 zr3644_9_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-Gene\n", " 2712951 zr3644_9_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-Gene\n", " 932568 zr3644_union-averages_5x.bedgraph-Meth.bed-Gene\n", " 615466 zr3644_union-averages_5x.bedgraph-sparseMeth.bed-Gene\n", " 4571088 zr3644_union-averages_5x.bedgraph-unMeth.bed-Gene\n", " 100709770 total\n" ] } ], "source": [ "#Count number of overlaps\n", "!wc -l *Gene" ] }, { "cell_type": "code", "execution_count": 46, "metadata": { "collapsed": false }, "outputs": [], "source": [ "#Get line counts for each fine\n", "# Remove 76th line (total entries)\n", "#Ensure output is tab-delimited\n", "#Save output\n", "!wc -l *-Gene \\\n", "| sed '76,$ d' \\\n", "| awk '{print $1\"\\t\"$2}' \\\n", "> zr3644_5x-Gene-counts.txt" ] }, { "cell_type": "code", "execution_count": 8, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "NC_047559.1\t10155\t10157\tNC_047559.1\tGnomon\tgene\t9839\t11386\t.\t+\t.\tID=gene-LOC117693020;Dbxref=GeneID:117693020;Name=LOC117693020;gbkey=Gene;gene=LOC117693020;gene_biotype=lncRNA\r\n", "NC_047559.1\t10215\t10217\tNC_047559.1\tGnomon\tgene\t9839\t11386\t.\t+\t.\tID=gene-LOC117693020;Dbxref=GeneID:117693020;Name=LOC117693020;gbkey=Gene;gene=LOC117693020;gene_biotype=lncRNA\r\n", "NC_047559.1\t10270\t10272\tNC_047559.1\tGnomon\tgene\t9839\t11386\t.\t+\t.\tID=gene-LOC117693020;Dbxref=GeneID:117693020;Name=LOC117693020;gbkey=Gene;gene=LOC117693020;gene_biotype=lncRNA\r\n", "NC_047559.1\t10292\t10294\tNC_047559.1\tGnomon\tgene\t9839\t11386\t.\t+\t.\tID=gene-LOC117693020;Dbxref=GeneID:117693020;Name=LOC117693020;gbkey=Gene;gene=LOC117693020;gene_biotype=lncRNA\r\n", "NC_047559.1\t10314\t10316\tNC_047559.1\tGnomon\tgene\t9839\t11386\t.\t+\t.\tID=gene-LOC117693020;Dbxref=GeneID:117693020;Name=LOC117693020;gbkey=Gene;gene=LOC117693020;gene_biotype=lncRNA\r\n", "NC_047559.1\t10358\t10360\tNC_047559.1\tGnomon\tgene\t9839\t11386\t.\t+\t.\tID=gene-LOC117693020;Dbxref=GeneID:117693020;Name=LOC117693020;gbkey=Gene;gene=LOC117693020;gene_biotype=lncRNA\r\n", "NC_047559.1\t10380\t10382\tNC_047559.1\tGnomon\tgene\t9839\t11386\t.\t+\t.\tID=gene-LOC117693020;Dbxref=GeneID:117693020;Name=LOC117693020;gbkey=Gene;gene=LOC117693020;gene_biotype=lncRNA\r\n", "NC_047559.1\t10391\t10393\tNC_047559.1\tGnomon\tgene\t9839\t11386\t.\t+\t.\tID=gene-LOC117693020;Dbxref=GeneID:117693020;Name=LOC117693020;gbkey=Gene;gene=LOC117693020;gene_biotype=lncRNA\r\n", "NC_047559.1\t10402\t10404\tNC_047559.1\tGnomon\tgene\t9839\t11386\t.\t+\t.\tID=gene-LOC117693020;Dbxref=GeneID:117693020;Name=LOC117693020;gbkey=Gene;gene=LOC117693020;gene_biotype=lncRNA\r\n", "NC_047559.1\t10413\t10415\tNC_047559.1\tGnomon\tgene\t9839\t11386\t.\t+\t.\tID=gene-LOC117693020;Dbxref=GeneID:117693020;Name=LOC117693020;gbkey=Gene;gene=LOC117693020;gene_biotype=lncRNA\r\n" ] } ], "source": [ "#Characterize overlap for downstream annotation\n", "!{bedtoolsDirectory}intersectBed \\\n", "-wb \\\n", "-a union_1x.bedgraph.bed \\\n", "-b /Volumes/web-1/halfshell/genomic-databank/cgigas_uk_roslin_v1_gene.gff \\\n", "> union_1x-Gene-wb.bed\n", "!head union_1x-Gene-wb.bed" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "### 6c. CDS" ] }, { "cell_type": "code", "execution_count": 6, "metadata": { "collapsed": false }, "outputs": [], "source": [ "%%bash\n", "for f in *bed\n", "do\n", " /Users/Shared/bioinformatics/bedtools2/bin/intersectBed \\\n", " -u \\\n", " -a ${f} \\\n", " -b /Volumes/web-1/halfshell/genomic-databank/cgigas_uk_roslin_v1_CDS.gff \\\n", " > ${f}-CDS\n", "done" ] }, { "cell_type": "code", "execution_count": 7, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "==> zr3644_10_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-CDS <==\n", "NC_047559.1\t433271\t433273\n", "NC_047559.1\t545968\t545970\n", "NC_047559.1\t548186\t548188\n", "NC_047559.1\t548188\t548190\n", "NC_047559.1\t548918\t548920\n", "NC_047559.1\t548941\t548943\n", "NC_047559.1\t548958\t548960\n", "NC_047559.1\t549827\t549829\n", "NC_047559.1\t549832\t549834\n", "NC_047559.1\t551729\t551731\n", "\n", "==> zr3644_10_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-CDS <==\n", "NC_047559.1\t123636\t123638\n", "NC_047559.1\t123655\t123657\n", "NC_047559.1\t139297\t139299\n", "NC_047559.1\t139334\t139336\n", "NC_047559.1\t139383\t139385\n", "NC_047559.1\t139389\t139391\n", "NC_047559.1\t139396\t139398\n", "NC_047559.1\t139430\t139432\n", "NC_047559.1\t139438\t139440\n", "NC_047559.1\t139443\t139445\n", "\n", "==> zr3644_10_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-CDS <==\n", "NC_047559.1\t14862\t14864\n", "NC_047559.1\t15162\t15164\n", "NC_047559.1\t15194\t15196\n", "NC_047559.1\t15204\t15206\n", "NC_047559.1\t15291\t15293\n", "NC_047559.1\t15293\t15295\n", "NC_047559.1\t15336\t15338\n", "NC_047559.1\t15338\t15340\n", "NC_047559.1\t15357\t15359\n", "NC_047559.1\t15370\t15372\n", "\n", "==> zr3644_11_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-CDS <==\n", "NC_047559.1\t139898\t139900\n", "NC_047559.1\t139912\t139914\n", "NC_047559.1\t139926\t139928\n", "NC_047559.1\t139945\t139947\n", "NC_047559.1\t139954\t139956\n", "NC_047559.1\t139972\t139974\n", "NC_047559.1\t139998\t140000\n", "NC_047559.1\t140007\t140009\n", "NC_047559.1\t140046\t140048\n", "NC_047559.1\t339030\t339032\n", "\n", "==> zr3644_11_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-CDS <==\n", "NC_047559.1\t17973\t17975\n", "NC_047559.1\t122491\t122493\n", "NC_047559.1\t139389\t139391\n", "NC_047559.1\t140083\t140085\n", "NC_047559.1\t140131\t140133\n", "NC_047559.1\t140139\t140141\n", "NC_047559.1\t140172\t140174\n", "NC_047559.1\t140424\t140426\n", "NC_047559.1\t140520\t140522\n", "NC_047559.1\t140539\t140541\n", "\n", "==> zr3644_11_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-CDS <==\n", "NC_047559.1\t14862\t14864\n", "NC_047559.1\t15162\t15164\n", "NC_047559.1\t15194\t15196\n", "NC_047559.1\t15204\t15206\n", "NC_047559.1\t15291\t15293\n", "NC_047559.1\t15293\t15295\n", "NC_047559.1\t15336\t15338\n", "NC_047559.1\t15338\t15340\n", "NC_047559.1\t15357\t15359\n", "NC_047559.1\t15370\t15372\n", "\n", "==> zr3644_12_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-CDS <==\n", "NC_047559.1\t433271\t433273\n", "NC_047559.1\t545968\t545970\n", "NC_047559.1\t548186\t548188\n", "NC_047559.1\t548188\t548190\n", "NC_047559.1\t548918\t548920\n", "NC_047559.1\t549827\t549829\n", "NC_047559.1\t549832\t549834\n", "NC_047559.1\t551729\t551731\n", "NC_047559.1\t551858\t551860\n", "NC_047559.1\t554065\t554067\n", "\n", "==> zr3644_12_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-CDS <==\n", "NC_047559.1\t140934\t140936\n", "NC_047559.1\t140963\t140965\n", "NC_047559.1\t140978\t140980\n", "NC_047559.1\t140984\t140986\n", "NC_047559.1\t141060\t141062\n", "NC_047559.1\t209598\t209600\n", "NC_047559.1\t338862\t338864\n", "NC_047559.1\t432606\t432608\n", "NC_047559.1\t432670\t432672\n", "NC_047559.1\t432696\t432698\n", "\n", "==> zr3644_12_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-CDS <==\n", "NC_047559.1\t14862\t14864\n", "NC_047559.1\t15194\t15196\n", "NC_047559.1\t15204\t15206\n", "NC_047559.1\t15336\t15338\n", "NC_047559.1\t15338\t15340\n", "NC_047559.1\t15357\t15359\n", "NC_047559.1\t15370\t15372\n", "NC_047559.1\t15407\t15409\n", "NC_047559.1\t15645\t15647\n", "NC_047559.1\t15656\t15658\n", "\n", "==> zr3644_13_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-CDS <==\n", "NC_047559.1\t139998\t140000\n", "NC_047559.1\t140007\t140009\n", "NC_047559.1\t338430\t338432\n", "NC_047559.1\t433316\t433318\n", "NC_047559.1\t545968\t545970\n", "NC_047559.1\t548186\t548188\n", "NC_047559.1\t548918\t548920\n", "NC_047559.1\t549827\t549829\n", "NC_047559.1\t549832\t549834\n", "NC_047559.1\t551729\t551731\n", "\n", "==> zr3644_13_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-CDS <==\n", "NC_047559.1\t139438\t139440\n", "NC_047559.1\t140046\t140048\n", "NC_047559.1\t140295\t140297\n", "NC_047559.1\t337326\t337328\n", "NC_047559.1\t337565\t337567\n", "NC_047559.1\t337616\t337618\n", "NC_047559.1\t337624\t337626\n", "NC_047559.1\t337639\t337641\n", "NC_047559.1\t337693\t337695\n", "NC_047559.1\t337706\t337708\n", "\n", "==> zr3644_13_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-CDS <==\n", "NC_047559.1\t14862\t14864\n", "NC_047559.1\t15162\t15164\n", "NC_047559.1\t15194\t15196\n", "NC_047559.1\t15204\t15206\n", "NC_047559.1\t15291\t15293\n", "NC_047559.1\t15293\t15295\n", "NC_047559.1\t15336\t15338\n", "NC_047559.1\t15338\t15340\n", "NC_047559.1\t15357\t15359\n", "NC_047559.1\t15370\t15372\n", "\n", "==> zr3644_14_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-CDS <==\n", "NC_047559.1\t432531\t432533\n", "NC_047559.1\t432606\t432608\n", "NC_047559.1\t432696\t432698\n", "NC_047559.1\t548186\t548188\n", "NC_047559.1\t548188\t548190\n", "NC_047559.1\t549827\t549829\n", "NC_047559.1\t549832\t549834\n", "NC_047559.1\t551729\t551731\n", "NC_047559.1\t551858\t551860\n", "NC_047559.1\t554065\t554067\n", "\n", "==> zr3644_14_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-CDS <==\n", "NC_047559.1\t139430\t139432\n", "NC_047559.1\t144144\t144146\n", "NC_047559.1\t327650\t327652\n", "NC_047559.1\t432670\t432672\n", "NC_047559.1\t432920\t432922\n", "NC_047559.1\t470759\t470761\n", "NC_047559.1\t562504\t562506\n", "NC_047559.1\t563598\t563600\n", "NC_047559.1\t565569\t565571\n", "NC_047559.1\t583166\t583168\n", "\n", "==> zr3644_14_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-CDS <==\n", "NC_047559.1\t14862\t14864\n", "NC_047559.1\t15162\t15164\n", "NC_047559.1\t15194\t15196\n", "NC_047559.1\t15204\t15206\n", "NC_047559.1\t15291\t15293\n", "NC_047559.1\t15293\t15295\n", "NC_047559.1\t15336\t15338\n", "NC_047559.1\t15338\t15340\n", "NC_047559.1\t15357\t15359\n", "NC_047559.1\t15370\t15372\n", "\n", "==> zr3644_15_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-CDS <==\n", "NC_047559.1\t99190\t99192\n", "NC_047559.1\t139972\t139974\n", "NC_047559.1\t139998\t140000\n", "NC_047559.1\t140007\t140009\n", "NC_047559.1\t140046\t140048\n", "NC_047559.1\t140539\t140541\n", "NC_047559.1\t140557\t140559\n", "NC_047559.1\t140589\t140591\n", "NC_047559.1\t140640\t140642\n", "NC_047559.1\t432531\t432533\n", "\n", "==> zr3644_15_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-CDS <==\n", "NC_047559.1\t139430\t139432\n", "NC_047559.1\t139438\t139440\n", "NC_047559.1\t140083\t140085\n", "NC_047559.1\t140284\t140286\n", "NC_047559.1\t140286\t140288\n", "NC_047559.1\t140292\t140294\n", "NC_047559.1\t140295\t140297\n", "NC_047559.1\t140377\t140379\n", "NC_047559.1\t140381\t140383\n", "NC_047559.1\t140894\t140896\n", "\n", "==> zr3644_15_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-CDS <==\n", "NC_047559.1\t14862\t14864\n", "NC_047559.1\t15162\t15164\n", "NC_047559.1\t15194\t15196\n", "NC_047559.1\t15204\t15206\n", "NC_047559.1\t15291\t15293\n", "NC_047559.1\t15293\t15295\n", "NC_047559.1\t15336\t15338\n", "NC_047559.1\t15338\t15340\n", "NC_047559.1\t15357\t15359\n", "NC_047559.1\t15370\t15372\n", "\n", "==> zr3644_16_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-CDS <==\n", "NC_047559.1\t338777\t338779\n", "NC_047559.1\t338819\t338821\n", "NC_047559.1\t338862\t338864\n", "NC_047559.1\t338883\t338885\n", "NC_047559.1\t339095\t339097\n", "NC_047559.1\t341533\t341535\n", "NC_047559.1\t341535\t341537\n", "NC_047559.1\t342302\t342304\n", "NC_047559.1\t342692\t342694\n", "NC_047559.1\t342699\t342701\n", "\n", "==> zr3644_16_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-CDS <==\n", "NC_047559.1\t80469\t80471\n", "NC_047559.1\t139430\t139432\n", "NC_047559.1\t139438\t139440\n", "NC_047559.1\t141298\t141300\n", "NC_047559.1\t337565\t337567\n", "NC_047559.1\t337616\t337618\n", "NC_047559.1\t337624\t337626\n", "NC_047559.1\t337639\t337641\n", "NC_047559.1\t337693\t337695\n", "NC_047559.1\t337706\t337708\n", "\n", "==> zr3644_16_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-CDS <==\n", "NC_047559.1\t14862\t14864\n", "NC_047559.1\t15162\t15164\n", "NC_047559.1\t15194\t15196\n", "NC_047559.1\t15204\t15206\n", "NC_047559.1\t15291\t15293\n", "NC_047559.1\t15293\t15295\n", "NC_047559.1\t15336\t15338\n", "NC_047559.1\t15338\t15340\n", "NC_047559.1\t15357\t15359\n", "NC_047559.1\t15370\t15372\n", "\n", "==> zr3644_17_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-CDS <==\n", "NC_047559.1\t337326\t337328\n", "NC_047559.1\t340780\t340782\n", "NC_047559.1\t340787\t340789\n", "NC_047559.1\t340813\t340815\n", "NC_047559.1\t432531\t432533\n", "NC_047559.1\t432920\t432922\n", "NC_047559.1\t433203\t433205\n", "NC_047559.1\t433271\t433273\n", "NC_047559.1\t433316\t433318\n", "NC_047559.1\t548148\t548150\n", "\n", "==> zr3644_17_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-CDS <==\n", "NC_047559.1\t139334\t139336\n", "NC_047559.1\t139383\t139385\n", "NC_047559.1\t139430\t139432\n", "NC_047559.1\t139438\t139440\n", "NC_047559.1\t139443\t139445\n", "NC_047559.1\t139520\t139522\n", "NC_047559.1\t140083\t140085\n", "NC_047559.1\t140172\t140174\n", "NC_047559.1\t337565\t337567\n", "NC_047559.1\t337616\t337618\n", "\n", "==> zr3644_17_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-CDS <==\n", "NC_047559.1\t14862\t14864\n", "NC_047559.1\t15099\t15101\n", "NC_047559.1\t15162\t15164\n", "NC_047559.1\t15194\t15196\n", "NC_047559.1\t15204\t15206\n", "NC_047559.1\t15291\t15293\n", "NC_047559.1\t15293\t15295\n", "NC_047559.1\t15336\t15338\n", "NC_047559.1\t15338\t15340\n", "NC_047559.1\t15357\t15359\n", "\n", "==> zr3644_18_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-CDS <==\n", "NC_047559.1\t139972\t139974\n", "NC_047559.1\t139998\t140000\n", "NC_047559.1\t140007\t140009\n", "NC_047559.1\t140046\t140048\n", "NC_047559.1\t140520\t140522\n", "NC_047559.1\t140539\t140541\n", "NC_047559.1\t140557\t140559\n", "NC_047559.1\t140589\t140591\n", "NC_047559.1\t140640\t140642\n", "NC_047559.1\t140894\t140896\n", "\n", "==> zr3644_18_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-CDS <==\n", "NC_047559.1\t122491\t122493\n", "NC_047559.1\t123648\t123650\n", "NC_047559.1\t139297\t139299\n", "NC_047559.1\t139334\t139336\n", "NC_047559.1\t139383\t139385\n", "NC_047559.1\t139389\t139391\n", "NC_047559.1\t139396\t139398\n", "NC_047559.1\t139430\t139432\n", "NC_047559.1\t139438\t139440\n", "NC_047559.1\t139443\t139445\n", "\n", "==> zr3644_18_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-CDS <==\n", "NC_047559.1\t14862\t14864\n", "NC_047559.1\t15162\t15164\n", "NC_047559.1\t15194\t15196\n", "NC_047559.1\t15204\t15206\n", "NC_047559.1\t15291\t15293\n", "NC_047559.1\t15293\t15295\n", "NC_047559.1\t15336\t15338\n", "NC_047559.1\t15338\t15340\n", "NC_047559.1\t15357\t15359\n", "NC_047559.1\t15370\t15372\n", "\n", "==> zr3644_19_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-CDS <==\n", "NC_047559.1\t140894\t140896\n", "NC_047559.1\t338777\t338779\n", "NC_047559.1\t338862\t338864\n", "NC_047559.1\t338883\t338885\n", "NC_047559.1\t340874\t340876\n", "NC_047559.1\t432531\t432533\n", "NC_047559.1\t432606\t432608\n", "NC_047559.1\t432670\t432672\n", "NC_047559.1\t432920\t432922\n", "NC_047559.1\t433316\t433318\n", "\n", "==> zr3644_19_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-CDS <==\n", "NC_047559.1\t14862\t14864\n", "NC_047559.1\t139297\t139299\n", "NC_047559.1\t139334\t139336\n", "NC_047559.1\t139389\t139391\n", "NC_047559.1\t139396\t139398\n", "NC_047559.1\t139438\t139440\n", "NC_047559.1\t139443\t139445\n", "NC_047559.1\t140934\t140936\n", "NC_047559.1\t140963\t140965\n", "NC_047559.1\t140978\t140980\n", "\n", "==> zr3644_19_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-CDS <==\n", "NC_047559.1\t15162\t15164\n", "NC_047559.1\t15194\t15196\n", "NC_047559.1\t15204\t15206\n", "NC_047559.1\t15291\t15293\n", "NC_047559.1\t15293\t15295\n", "NC_047559.1\t15336\t15338\n", "NC_047559.1\t15338\t15340\n", "NC_047559.1\t15357\t15359\n", "NC_047559.1\t15370\t15372\n", "NC_047559.1\t15407\t15409\n", "\n", "==> zr3644_1_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-CDS <==\n", "NC_047559.1\t338430\t338432\n", "NC_047559.1\t338444\t338446\n", "NC_047559.1\t432531\t432533\n", "NC_047559.1\t432606\t432608\n", "NC_047559.1\t432670\t432672\n", "NC_047559.1\t432696\t432698\n", "NC_047559.1\t432920\t432922\n", "NC_047559.1\t433203\t433205\n", "NC_047559.1\t433271\t433273\n", "NC_047559.1\t545968\t545970\n", "\n", "==> zr3644_1_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-CDS <==\n", "NC_047559.1\t15162\t15164\n", "NC_047559.1\t84364\t84366\n", "NC_047559.1\t337565\t337567\n", "NC_047559.1\t337616\t337618\n", "NC_047559.1\t337624\t337626\n", "NC_047559.1\t337639\t337641\n", "NC_047559.1\t337693\t337695\n", "NC_047559.1\t337706\t337708\n", "NC_047559.1\t337746\t337748\n", "NC_047559.1\t337766\t337768\n", "\n", "==> zr3644_1_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-CDS <==\n", "NC_047559.1\t15194\t15196\n", "NC_047559.1\t15204\t15206\n", "NC_047559.1\t15291\t15293\n", "NC_047559.1\t15293\t15295\n", "NC_047559.1\t15336\t15338\n", "NC_047559.1\t15338\t15340\n", "NC_047559.1\t15357\t15359\n", "NC_047559.1\t15370\t15372\n", "NC_047559.1\t15407\t15409\n", "NC_047559.1\t15645\t15647\n", "\n", "==> zr3644_20_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-CDS <==\n", "NC_047559.1\t433203\t433205\n", "NC_047559.1\t433271\t433273\n", "NC_047559.1\t433316\t433318\n", "NC_047559.1\t545968\t545970\n", "NC_047559.1\t548148\t548150\n", "NC_047559.1\t548918\t548920\n", "NC_047559.1\t549827\t549829\n", "NC_047559.1\t549832\t549834\n", "NC_047559.1\t551729\t551731\n", "NC_047559.1\t551858\t551860\n", "\n", "==> zr3644_20_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-CDS <==\n", "NC_047559.1\t209440\t209442\n", "NC_047559.1\t372670\t372672\n", "NC_047559.1\t432531\t432533\n", "NC_047559.1\t432606\t432608\n", "NC_047559.1\t432670\t432672\n", "NC_047559.1\t432696\t432698\n", "NC_047559.1\t432851\t432853\n", "NC_047559.1\t432920\t432922\n", "NC_047559.1\t470791\t470793\n", "NC_047559.1\t475302\t475304\n", "\n", "==> zr3644_20_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-CDS <==\n", "NC_047559.1\t14862\t14864\n", "NC_047559.1\t15162\t15164\n", "NC_047559.1\t15194\t15196\n", "NC_047559.1\t15204\t15206\n", "NC_047559.1\t15291\t15293\n", "NC_047559.1\t15293\t15295\n", "NC_047559.1\t15336\t15338\n", "NC_047559.1\t15338\t15340\n", "NC_047559.1\t15357\t15359\n", "NC_047559.1\t15370\t15372\n", "\n", "==> zr3644_21_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-CDS <==\n", "NC_047559.1\t432531\t432533\n", "NC_047559.1\t432670\t432672\n", "NC_047559.1\t432696\t432698\n", "NC_047559.1\t433203\t433205\n", "NC_047559.1\t433271\t433273\n", "NC_047559.1\t548148\t548150\n", "NC_047559.1\t549827\t549829\n", "NC_047559.1\t549832\t549834\n", "NC_047559.1\t551729\t551731\n", "NC_047559.1\t551858\t551860\n", "\n", "==> zr3644_21_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-CDS <==\n", "NC_047559.1\t140377\t140379\n", "NC_047559.1\t140381\t140383\n", "NC_047559.1\t140557\t140559\n", "NC_047559.1\t140589\t140591\n", "NC_047559.1\t140894\t140896\n", "NC_047559.1\t140934\t140936\n", "NC_047559.1\t140963\t140965\n", "NC_047559.1\t140978\t140980\n", "NC_047559.1\t140984\t140986\n", "NC_047559.1\t141060\t141062\n", "\n", "==> zr3644_21_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-CDS <==\n", "NC_047559.1\t14862\t14864\n", "NC_047559.1\t15099\t15101\n", "NC_047559.1\t15162\t15164\n", "NC_047559.1\t15194\t15196\n", "NC_047559.1\t15204\t15206\n", "NC_047559.1\t15291\t15293\n", "NC_047559.1\t15293\t15295\n", "NC_047559.1\t15336\t15338\n", "NC_047559.1\t15338\t15340\n", "NC_047559.1\t15357\t15359\n", "\n", "==> zr3644_22_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-CDS <==\n", "NC_047559.1\t432531\t432533\n", "NC_047559.1\t432606\t432608\n", "NC_047559.1\t432670\t432672\n", "NC_047559.1\t432696\t432698\n", "NC_047559.1\t433203\t433205\n", "NC_047559.1\t548186\t548188\n", "NC_047559.1\t548188\t548190\n", "NC_047559.1\t548918\t548920\n", "NC_047559.1\t548941\t548943\n", "NC_047559.1\t548958\t548960\n", "\n", "==> zr3644_22_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-CDS <==\n", "NC_047559.1\t123636\t123638\n", "NC_047559.1\t139334\t139336\n", "NC_047559.1\t139430\t139432\n", "NC_047559.1\t139438\t139440\n", "NC_047559.1\t139443\t139445\n", "NC_047559.1\t140520\t140522\n", "NC_047559.1\t140539\t140541\n", "NC_047559.1\t140557\t140559\n", "NC_047559.1\t140589\t140591\n", "NC_047559.1\t140963\t140965\n", "\n", "==> zr3644_22_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-CDS <==\n", "NC_047559.1\t14862\t14864\n", "NC_047559.1\t15162\t15164\n", "NC_047559.1\t15194\t15196\n", "NC_047559.1\t15204\t15206\n", "NC_047559.1\t15291\t15293\n", "NC_047559.1\t15293\t15295\n", "NC_047559.1\t15336\t15338\n", "NC_047559.1\t15338\t15340\n", "NC_047559.1\t15357\t15359\n", "NC_047559.1\t15370\t15372\n", "\n", "==> zr3644_23_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-CDS <==\n", "NC_047559.1\t432531\t432533\n", "NC_047559.1\t432606\t432608\n", "NC_047559.1\t432670\t432672\n", "NC_047559.1\t432696\t432698\n", "NC_047559.1\t432920\t432922\n", "NC_047559.1\t433154\t433156\n", "NC_047559.1\t433203\t433205\n", "NC_047559.1\t433271\t433273\n", "NC_047559.1\t545968\t545970\n", "NC_047559.1\t548186\t548188\n", "\n", "==> zr3644_23_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-CDS <==\n", "NC_047559.1\t123489\t123491\n", "NC_047559.1\t140083\t140085\n", "NC_047559.1\t140377\t140379\n", "NC_047559.1\t140381\t140383\n", "NC_047559.1\t140424\t140426\n", "NC_047559.1\t140589\t140591\n", "NC_047559.1\t140934\t140936\n", "NC_047559.1\t140963\t140965\n", "NC_047559.1\t140978\t140980\n", "NC_047559.1\t140984\t140986\n", "\n", "==> zr3644_23_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-CDS <==\n", "NC_047559.1\t14862\t14864\n", "NC_047559.1\t15162\t15164\n", "NC_047559.1\t15194\t15196\n", "NC_047559.1\t15204\t15206\n", "NC_047559.1\t15291\t15293\n", "NC_047559.1\t15293\t15295\n", "NC_047559.1\t15336\t15338\n", "NC_047559.1\t15338\t15340\n", "NC_047559.1\t15357\t15359\n", "NC_047559.1\t15370\t15372\n", "\n", "==> zr3644_24_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-CDS <==\n", "NC_047559.1\t432531\t432533\n", "NC_047559.1\t432606\t432608\n", "NC_047559.1\t432670\t432672\n", "NC_047559.1\t432696\t432698\n", "NC_047559.1\t432920\t432922\n", "NC_047559.1\t433203\t433205\n", "NC_047559.1\t433271\t433273\n", "NC_047559.1\t545968\t545970\n", "NC_047559.1\t548186\t548188\n", "NC_047559.1\t548188\t548190\n", "\n", "==> zr3644_24_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-CDS <==\n", "NC_047559.1\t139396\t139398\n", "NC_047559.1\t139430\t139432\n", "NC_047559.1\t139438\t139440\n", "NC_047559.1\t139443\t139445\n", "NC_047559.1\t140046\t140048\n", "NC_047559.1\t140083\t140085\n", "NC_047559.1\t140381\t140383\n", "NC_047559.1\t140589\t140591\n", "NC_047559.1\t140640\t140642\n", "NC_047559.1\t141060\t141062\n", "\n", "==> zr3644_24_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-CDS <==\n", "NC_047559.1\t14862\t14864\n", "NC_047559.1\t15162\t15164\n", "NC_047559.1\t15194\t15196\n", "NC_047559.1\t15204\t15206\n", "NC_047559.1\t15291\t15293\n", "NC_047559.1\t15293\t15295\n", "NC_047559.1\t15336\t15338\n", "NC_047559.1\t15338\t15340\n", "NC_047559.1\t15357\t15359\n", "NC_047559.1\t15370\t15372\n", "\n", "==> zr3644_2_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-CDS <==\n", "NC_047559.1\t432670\t432672\n", "NC_047559.1\t432696\t432698\n", "NC_047559.1\t432920\t432922\n", "NC_047559.1\t433203\t433205\n", "NC_047559.1\t433316\t433318\n", "NC_047559.1\t545968\t545970\n", "NC_047559.1\t548918\t548920\n", "NC_047559.1\t549827\t549829\n", "NC_047559.1\t549832\t549834\n", "NC_047559.1\t551729\t551731\n", "\n", "==> zr3644_2_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-CDS <==\n", "NC_047559.1\t139396\t139398\n", "NC_047559.1\t337565\t337567\n", "NC_047559.1\t337706\t337708\n", "NC_047559.1\t337746\t337748\n", "NC_047559.1\t337766\t337768\n", "NC_047559.1\t337788\t337790\n", "NC_047559.1\t337972\t337974\n", "NC_047559.1\t337977\t337979\n", "NC_047559.1\t338021\t338023\n", "NC_047559.1\t338057\t338059\n", "\n", "==> zr3644_2_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-CDS <==\n", "NC_047559.1\t14862\t14864\n", "NC_047559.1\t15099\t15101\n", "NC_047559.1\t15162\t15164\n", "NC_047559.1\t15194\t15196\n", "NC_047559.1\t15204\t15206\n", "NC_047559.1\t15291\t15293\n", "NC_047559.1\t15293\t15295\n", "NC_047559.1\t15336\t15338\n", "NC_047559.1\t15338\t15340\n", "NC_047559.1\t15357\t15359\n", "\n", "==> zr3644_3_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-CDS <==\n", "NC_047559.1\t338430\t338432\n", "NC_047559.1\t338444\t338446\n", "NC_047559.1\t338617\t338619\n", "NC_047559.1\t340912\t340914\n", "NC_047559.1\t340923\t340925\n", "NC_047559.1\t341839\t341841\n", "NC_047559.1\t342246\t342248\n", "NC_047559.1\t342250\t342252\n", "NC_047559.1\t432531\t432533\n", "NC_047559.1\t432606\t432608\n", "\n", "==> zr3644_3_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-CDS <==\n", "NC_047559.1\t337565\t337567\n", "NC_047559.1\t337616\t337618\n", "NC_047559.1\t337624\t337626\n", "NC_047559.1\t337639\t337641\n", "NC_047559.1\t337693\t337695\n", "NC_047559.1\t337706\t337708\n", "NC_047559.1\t337746\t337748\n", "NC_047559.1\t337766\t337768\n", "NC_047559.1\t337788\t337790\n", "NC_047559.1\t337854\t337856\n", "\n", "==> zr3644_3_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-CDS <==\n", "NC_047559.1\t14862\t14864\n", "NC_047559.1\t15162\t15164\n", "NC_047559.1\t15194\t15196\n", "NC_047559.1\t15204\t15206\n", "NC_047559.1\t15291\t15293\n", "NC_047559.1\t15293\t15295\n", "NC_047559.1\t15336\t15338\n", "NC_047559.1\t15338\t15340\n", "NC_047559.1\t15357\t15359\n", "NC_047559.1\t15370\t15372\n", "\n", "==> zr3644_4_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-CDS <==\n", "NC_047559.1\t432606\t432608\n", "NC_047559.1\t432670\t432672\n", "NC_047559.1\t432696\t432698\n", "NC_047559.1\t432851\t432853\n", "NC_047559.1\t432920\t432922\n", "NC_047559.1\t433154\t433156\n", "NC_047559.1\t433203\t433205\n", "NC_047559.1\t433271\t433273\n", "NC_047559.1\t433316\t433318\n", "NC_047559.1\t548918\t548920\n", "\n", "==> zr3644_4_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-CDS <==\n", "NC_047559.1\t18003\t18005\n", "NC_047559.1\t139430\t139432\n", "NC_047559.1\t139438\t139440\n", "NC_047559.1\t139443\t139445\n", "NC_047559.1\t266657\t266659\n", "NC_047559.1\t337972\t337974\n", "NC_047559.1\t337977\t337979\n", "NC_047559.1\t338021\t338023\n", "NC_047559.1\t338057\t338059\n", "NC_047559.1\t338430\t338432\n", "\n", "==> zr3644_4_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-CDS <==\n", "NC_047559.1\t14862\t14864\n", "NC_047559.1\t15162\t15164\n", "NC_047559.1\t15194\t15196\n", "NC_047559.1\t15204\t15206\n", "NC_047559.1\t15291\t15293\n", "NC_047559.1\t15293\t15295\n", "NC_047559.1\t15336\t15338\n", "NC_047559.1\t15338\t15340\n", "NC_047559.1\t15357\t15359\n", "NC_047559.1\t15370\t15372\n", "\n", "==> zr3644_5_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-CDS <==\n", "NC_047559.1\t140539\t140541\n", "NC_047559.1\t140557\t140559\n", "NC_047559.1\t140589\t140591\n", "NC_047559.1\t140640\t140642\n", "NC_047559.1\t432606\t432608\n", "NC_047559.1\t432670\t432672\n", "NC_047559.1\t432920\t432922\n", "NC_047559.1\t433203\t433205\n", "NC_047559.1\t433316\t433318\n", "NC_047559.1\t545968\t545970\n", "\n", "==> zr3644_5_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-CDS <==\n", "NC_047559.1\t80725\t80727\n", "NC_047559.1\t80737\t80739\n", "NC_047559.1\t139972\t139974\n", "NC_047559.1\t139998\t140000\n", "NC_047559.1\t140007\t140009\n", "NC_047559.1\t140046\t140048\n", "NC_047559.1\t140083\t140085\n", "NC_047559.1\t140139\t140141\n", "NC_047559.1\t140377\t140379\n", "NC_047559.1\t140381\t140383\n", "\n", "==> zr3644_5_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-CDS <==\n", "NC_047559.1\t14862\t14864\n", "NC_047559.1\t15099\t15101\n", "NC_047559.1\t15162\t15164\n", "NC_047559.1\t15194\t15196\n", "NC_047559.1\t15204\t15206\n", "NC_047559.1\t15291\t15293\n", "NC_047559.1\t15293\t15295\n", "NC_047559.1\t15336\t15338\n", "NC_047559.1\t15338\t15340\n", "NC_047559.1\t15357\t15359\n", "\n", "==> zr3644_6_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-CDS <==\n", "NC_047559.1\t139945\t139947\n", "NC_047559.1\t139954\t139956\n", "NC_047559.1\t139972\t139974\n", "NC_047559.1\t139998\t140000\n", "NC_047559.1\t140539\t140541\n", "NC_047559.1\t140557\t140559\n", "NC_047559.1\t140589\t140591\n", "NC_047559.1\t337624\t337626\n", "NC_047559.1\t337639\t337641\n", "NC_047559.1\t341781\t341783\n", "\n", "==> zr3644_6_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-CDS <==\n", "NC_047559.1\t140007\t140009\n", "NC_047559.1\t140046\t140048\n", "NC_047559.1\t140083\t140085\n", "NC_047559.1\t140131\t140133\n", "NC_047559.1\t140139\t140141\n", "NC_047559.1\t140172\t140174\n", "NC_047559.1\t140334\t140336\n", "NC_047559.1\t140508\t140510\n", "NC_047559.1\t140520\t140522\n", "NC_047559.1\t140640\t140642\n", "\n", "==> zr3644_6_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-CDS <==\n", "NC_047559.1\t14862\t14864\n", "NC_047559.1\t15162\t15164\n", "NC_047559.1\t15194\t15196\n", "NC_047559.1\t15204\t15206\n", "NC_047559.1\t15291\t15293\n", "NC_047559.1\t15293\t15295\n", "NC_047559.1\t15336\t15338\n", "NC_047559.1\t15338\t15340\n", "NC_047559.1\t15357\t15359\n", "NC_047559.1\t15370\t15372\n", "\n", "==> zr3644_7_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-CDS <==\n", "NC_047559.1\t140589\t140591\n", "NC_047559.1\t140640\t140642\n", "NC_047559.1\t432531\t432533\n", "NC_047559.1\t432606\t432608\n", "NC_047559.1\t432670\t432672\n", "NC_047559.1\t432696\t432698\n", "NC_047559.1\t432851\t432853\n", "NC_047559.1\t432920\t432922\n", "NC_047559.1\t433154\t433156\n", "NC_047559.1\t545968\t545970\n", "\n", "==> zr3644_7_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-CDS <==\n", "NC_047559.1\t139396\t139398\n", "NC_047559.1\t139430\t139432\n", "NC_047559.1\t139438\t139440\n", "NC_047559.1\t139443\t139445\n", "NC_047559.1\t139520\t139522\n", "NC_047559.1\t139529\t139531\n", "NC_047559.1\t139554\t139556\n", "NC_047559.1\t139585\t139587\n", "NC_047559.1\t139590\t139592\n", "NC_047559.1\t139898\t139900\n", "\n", "==> zr3644_7_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-CDS <==\n", "NC_047559.1\t14862\t14864\n", "NC_047559.1\t15162\t15164\n", "NC_047559.1\t15194\t15196\n", "NC_047559.1\t15204\t15206\n", "NC_047559.1\t15291\t15293\n", "NC_047559.1\t15293\t15295\n", "NC_047559.1\t15336\t15338\n", "NC_047559.1\t15338\t15340\n", "NC_047559.1\t15357\t15359\n", "NC_047559.1\t15370\t15372\n", "\n", "==> zr3644_8_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-CDS <==\n", "NC_047559.1\t432531\t432533\n", "NC_047559.1\t432606\t432608\n", "NC_047559.1\t432670\t432672\n", "NC_047559.1\t432920\t432922\n", "NC_047559.1\t433271\t433273\n", "NC_047559.1\t475394\t475396\n", "NC_047559.1\t545968\t545970\n", "NC_047559.1\t548186\t548188\n", "NC_047559.1\t548188\t548190\n", "NC_047559.1\t548918\t548920\n", "\n", "==> zr3644_8_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-CDS <==\n", "NC_047559.1\t139430\t139432\n", "NC_047559.1\t182414\t182416\n", "NC_047559.1\t182417\t182419\n", "NC_047559.1\t327533\t327535\n", "NC_047559.1\t337565\t337567\n", "NC_047559.1\t337616\t337618\n", "NC_047559.1\t337624\t337626\n", "NC_047559.1\t337639\t337641\n", "NC_047559.1\t337746\t337748\n", "NC_047559.1\t337766\t337768\n", "\n", "==> zr3644_8_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-CDS <==\n", "NC_047559.1\t14862\t14864\n", "NC_047559.1\t14964\t14966\n", "NC_047559.1\t15291\t15293\n", "NC_047559.1\t15293\t15295\n", "NC_047559.1\t15336\t15338\n", "NC_047559.1\t15338\t15340\n", "NC_047559.1\t15357\t15359\n", "NC_047559.1\t15370\t15372\n", "NC_047559.1\t15407\t15409\n", "NC_047559.1\t15645\t15647\n", "\n", "==> zr3644_9_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-CDS <==\n", "NC_047559.1\t140520\t140522\n", "NC_047559.1\t140539\t140541\n", "NC_047559.1\t140557\t140559\n", "NC_047559.1\t140589\t140591\n", "NC_047559.1\t140640\t140642\n", "NC_047559.1\t432531\t432533\n", "NC_047559.1\t432606\t432608\n", "NC_047559.1\t432670\t432672\n", "NC_047559.1\t432696\t432698\n", "NC_047559.1\t432851\t432853\n", "\n", "==> zr3644_9_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-CDS <==\n", "NC_047559.1\t140377\t140379\n", "NC_047559.1\t140381\t140383\n", "NC_047559.1\t140424\t140426\n", "NC_047559.1\t140934\t140936\n", "NC_047559.1\t140963\t140965\n", "NC_047559.1\t140978\t140980\n", "NC_047559.1\t140984\t140986\n", "NC_047559.1\t141060\t141062\n", "NC_047559.1\t141341\t141343\n", "NC_047559.1\t209509\t209511\n", "\n", "==> zr3644_9_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-CDS <==\n", "NC_047559.1\t15370\t15372\n", "NC_047559.1\t15407\t15409\n", "NC_047559.1\t15645\t15647\n", "NC_047559.1\t15656\t15658\n", "NC_047559.1\t15674\t15676\n", "NC_047559.1\t15678\t15680\n", "NC_047559.1\t15680\t15682\n", "NC_047559.1\t15746\t15748\n", "NC_047559.1\t18003\t18005\n", "NC_047559.1\t18024\t18026\n", "\n", "==> zr3644_union-averages_5x.bedgraph-Meth.bed-CDS <==\n", "NC_047559.1\t139898\t139900\n", "NC_047559.1\t139912\t139914\n", "NC_047559.1\t139926\t139928\n", "NC_047559.1\t139945\t139947\n", "NC_047559.1\t139954\t139956\n", "NC_047559.1\t139972\t139974\n", "NC_047559.1\t140539\t140541\n", "NC_047559.1\t432531\t432533\n", "NC_047559.1\t432670\t432672\n", "NC_047559.1\t432696\t432698\n", "\n", "==> zr3644_union-averages_5x.bedgraph-sparseMeth.bed-CDS <==\n", "NC_047559.1\t139430\t139432\n", "NC_047559.1\t139520\t139522\n", "NC_047559.1\t139529\t139531\n", "NC_047559.1\t139554\t139556\n", "NC_047559.1\t139585\t139587\n", "NC_047559.1\t139590\t139592\n", "NC_047559.1\t139998\t140000\n", "NC_047559.1\t140007\t140009\n", "NC_047559.1\t140046\t140048\n", "NC_047559.1\t140083\t140085\n", "\n", "==> zr3644_union-averages_5x.bedgraph-unMeth.bed-CDS <==\n", "NC_047559.1\t14862\t14864\n", "NC_047559.1\t14964\t14966\n", "NC_047559.1\t15099\t15101\n", "NC_047559.1\t15162\t15164\n", "NC_047559.1\t15194\t15196\n", "NC_047559.1\t15204\t15206\n", "NC_047559.1\t15291\t15293\n", "NC_047559.1\t15293\t15295\n", "NC_047559.1\t15336\t15338\n", "NC_047559.1\t15338\t15340\n" ] } ], "source": [ "#Check output\n", "!head *CDS" ] }, { "cell_type": "code", "execution_count": 8, "metadata": { "collapsed": false, "scrolled": true }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ " 303330 zr3644_10_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-CDS\n", " 63358 zr3644_10_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-CDS\n", " 754584 zr3644_10_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-CDS\n", " 304639 zr3644_11_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-CDS\n", " 67810 zr3644_11_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-CDS\n", " 769482 zr3644_11_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-CDS\n", " 241585 zr3644_12_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-CDS\n", " 59366 zr3644_12_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-CDS\n", " 686708 zr3644_12_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-CDS\n", " 298469 zr3644_13_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-CDS\n", " 69735 zr3644_13_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-CDS\n", " 755670 zr3644_13_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-CDS\n", " 258769 zr3644_14_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-CDS\n", " 43881 zr3644_14_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-CDS\n", " 656211 zr3644_14_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-CDS\n", " 317809 zr3644_15_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-CDS\n", " 60859 zr3644_15_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-CDS\n", " 775242 zr3644_15_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-CDS\n", " 288664 zr3644_16_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-CDS\n", " 63922 zr3644_16_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-CDS\n", " 732043 zr3644_16_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-CDS\n", " 300098 zr3644_17_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-CDS\n", " 61456 zr3644_17_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-CDS\n", " 767977 zr3644_17_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-CDS\n", " 294141 zr3644_18_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-CDS\n", " 70806 zr3644_18_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-CDS\n", " 749289 zr3644_18_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-CDS\n", " 286761 zr3644_19_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-CDS\n", " 65072 zr3644_19_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-CDS\n", " 741378 zr3644_19_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-CDS\n", " 268364 zr3644_1_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-CDS\n", " 80563 zr3644_1_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-CDS\n", " 735595 zr3644_1_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-CDS\n", " 296095 zr3644_20_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-CDS\n", " 68282 zr3644_20_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-CDS\n", " 756151 zr3644_20_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-CDS\n", " 292462 zr3644_21_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-CDS\n", " 68432 zr3644_21_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-CDS\n", " 746397 zr3644_21_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-CDS\n", " 286510 zr3644_22_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-CDS\n", " 66901 zr3644_22_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-CDS\n", " 733032 zr3644_22_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-CDS\n", " 260128 zr3644_23_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-CDS\n", " 62003 zr3644_23_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-CDS\n", " 682544 zr3644_23_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-CDS\n", " 294915 zr3644_24_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-CDS\n", " 66671 zr3644_24_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-CDS\n", " 755798 zr3644_24_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-CDS\n", " 294774 zr3644_2_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-CDS\n", " 60862 zr3644_2_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-CDS\n", " 763625 zr3644_2_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-CDS\n", " 257445 zr3644_3_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-CDS\n", " 61363 zr3644_3_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-CDS\n", " 673919 zr3644_3_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-CDS\n", " 281072 zr3644_4_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-CDS\n", " 66249 zr3644_4_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-CDS\n", " 735356 zr3644_4_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-CDS\n", " 276260 zr3644_5_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-CDS\n", " 66326 zr3644_5_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-CDS\n", " 714272 zr3644_5_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-CDS\n", " 296355 zr3644_6_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-CDS\n", " 66826 zr3644_6_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-CDS\n", " 758322 zr3644_6_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-CDS\n", " 329807 zr3644_7_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-CDS\n", " 70448 zr3644_7_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-CDS\n", " 831137 zr3644_7_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-CDS\n", " 272142 zr3644_8_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-CDS\n", " 62538 zr3644_8_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-CDS\n", " 700302 zr3644_8_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-CDS\n", " 287293 zr3644_9_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-CDS\n", " 65482 zr3644_9_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-CDS\n", " 717924 zr3644_9_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-CDS\n", " 353333 zr3644_union-averages_5x.bedgraph-Meth.bed-CDS\n", " 78651 zr3644_union-averages_5x.bedgraph-sparseMeth.bed-CDS\n", " 936647 zr3644_union-averages_5x.bedgraph-unMeth.bed-CDS\n", " 27508687 total\n" ] } ], "source": [ "#Count number of overlaps\n", "!wc -l *CDS" ] }, { "cell_type": "code", "execution_count": 9, "metadata": { "collapsed": false }, "outputs": [], "source": [ "#Get line counts for each fine\n", "# Remove 76th line (total entries)\n", "#Ensure output is tab-delimited\n", "#Save output\n", "!wc -l *-CDS \\\n", "| sed '76,$ d' \\\n", "| awk '{print $1\"\\t\"$2}' \\\n", "> zr3644_5x-CDS-counts.txt" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "### 6d. Exon UTR" ] }, { "cell_type": "code", "execution_count": 47, "metadata": { "collapsed": false }, "outputs": [], "source": [ "%%bash\n", "for f in *bed\n", "do\n", " /Users/Shared/bioinformatics/bedtools2/bin/intersectBed \\\n", " -u \\\n", " -a ${f} \\\n", " -b /Volumes/web-1/halfshell/genomic-databank/cgigas_uk_roslin_v1_exonUTR.gff \\\n", " > ${f}-exonUTR\n", "done" ] }, { "cell_type": "code", "execution_count": 48, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "==> zr3644_10_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-exonUTR <==\n", "NC_047559.1\t416078\t416080\n", "NC_047559.1\t418539\t418541\n", "NC_047559.1\t544784\t544786\n", "NC_047559.1\t571583\t571585\n", "NC_047559.1\t571793\t571795\n", "NC_047559.1\t571838\t571840\n", "NC_047559.1\t571906\t571908\n", "NC_047559.1\t571929\t571931\n", "NC_047559.1\t572049\t572051\n", "NC_047559.1\t572075\t572077\n", "\n", "==> zr3644_10_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-exonUTR <==\n", "NC_047559.1\t416052\t416054\n", "NC_047559.1\t416071\t416073\n", "NC_047559.1\t416088\t416090\n", "NC_047559.1\t431124\t431126\n", "NC_047559.1\t469758\t469760\n", "NC_047559.1\t545687\t545689\n", "NC_047559.1\t560332\t560334\n", "NC_047559.1\t572153\t572155\n", "NC_047559.1\t572900\t572902\n", "NC_047559.1\t597401\t597403\n", "\n", "==> zr3644_10_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-exonUTR <==\n", "NC_047559.1\t10899\t10901\n", "NC_047559.1\t10920\t10922\n", "NC_047559.1\t10950\t10952\n", "NC_047559.1\t11000\t11002\n", "NC_047559.1\t11026\t11028\n", "NC_047559.1\t14214\t14216\n", "NC_047559.1\t14232\t14234\n", "NC_047559.1\t14243\t14245\n", "NC_047559.1\t14259\t14261\n", "NC_047559.1\t14319\t14321\n", "\n", "==> zr3644_11_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-exonUTR <==\n", "NC_047559.1\t544387\t544389\n", "NC_047559.1\t545687\t545689\n", "NC_047559.1\t571838\t571840\n", "NC_047559.1\t571906\t571908\n", "NC_047559.1\t571929\t571931\n", "NC_047559.1\t572049\t572051\n", "NC_047559.1\t572075\t572077\n", "NC_047559.1\t572153\t572155\n", "NC_047559.1\t572263\t572265\n", "NC_047559.1\t572332\t572334\n", "\n", "==> zr3644_11_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-exonUTR <==\n", "NC_047559.1\t337166\t337168\n", "NC_047559.1\t343479\t343481\n", "NC_047559.1\t343574\t343576\n", "NC_047559.1\t343603\t343605\n", "NC_047559.1\t431124\t431126\n", "NC_047559.1\t431205\t431207\n", "NC_047559.1\t473159\t473161\n", "NC_047559.1\t544404\t544406\n", "NC_047559.1\t544552\t544554\n", "NC_047559.1\t544592\t544594\n", "\n", "==> zr3644_11_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-exonUTR <==\n", "NC_047559.1\t10899\t10901\n", "NC_047559.1\t10920\t10922\n", "NC_047559.1\t10950\t10952\n", "NC_047559.1\t11000\t11002\n", "NC_047559.1\t11026\t11028\n", "NC_047559.1\t14214\t14216\n", "NC_047559.1\t14232\t14234\n", "NC_047559.1\t14243\t14245\n", "NC_047559.1\t14259\t14261\n", "NC_047559.1\t14319\t14321\n", "\n", "==> zr3644_12_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-exonUTR <==\n", "NC_047559.1\t431205\t431207\n", "NC_047559.1\t544784\t544786\n", "NC_047559.1\t545229\t545231\n", "NC_047559.1\t545256\t545258\n", "NC_047559.1\t571838\t571840\n", "NC_047559.1\t571906\t571908\n", "NC_047559.1\t571929\t571931\n", "NC_047559.1\t572049\t572051\n", "NC_047559.1\t572245\t572247\n", "NC_047559.1\t572557\t572559\n", "\n", "==> zr3644_12_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-exonUTR <==\n", "NC_047559.1\t19113\t19115\n", "NC_047559.1\t204905\t204907\n", "NC_047559.1\t431124\t431126\n", "NC_047559.1\t544592\t544594\n", "NC_047559.1\t571583\t571585\n", "NC_047559.1\t596489\t596491\n", "NC_047559.1\t597401\t597403\n", "NC_047559.1\t601710\t601712\n", "NC_047559.1\t602021\t602023\n", "NC_047559.1\t602052\t602054\n", "\n", "==> zr3644_12_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-exonUTR <==\n", "NC_047559.1\t10899\t10901\n", "NC_047559.1\t10920\t10922\n", "NC_047559.1\t10950\t10952\n", "NC_047559.1\t11000\t11002\n", "NC_047559.1\t11026\t11028\n", "NC_047559.1\t11080\t11082\n", "NC_047559.1\t14214\t14216\n", "NC_047559.1\t14232\t14234\n", "NC_047559.1\t14243\t14245\n", "NC_047559.1\t14259\t14261\n", "\n", "==> zr3644_13_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-exonUTR <==\n", "NC_047559.1\t416088\t416090\n", "NC_047559.1\t545229\t545231\n", "NC_047559.1\t545256\t545258\n", "NC_047559.1\t571793\t571795\n", "NC_047559.1\t571906\t571908\n", "NC_047559.1\t571929\t571931\n", "NC_047559.1\t572153\t572155\n", "NC_047559.1\t572233\t572235\n", "NC_047559.1\t572245\t572247\n", "NC_047559.1\t572263\t572265\n", "\n", "==> zr3644_13_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-exonUTR <==\n", "NC_047559.1\t343538\t343540\n", "NC_047559.1\t415957\t415959\n", "NC_047559.1\t415975\t415977\n", "NC_047559.1\t415988\t415990\n", "NC_047559.1\t415998\t416000\n", "NC_047559.1\t416052\t416054\n", "NC_047559.1\t416071\t416073\n", "NC_047559.1\t418539\t418541\n", "NC_047559.1\t431124\t431126\n", "NC_047559.1\t431205\t431207\n", "\n", "==> zr3644_13_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-exonUTR <==\n", "NC_047559.1\t10899\t10901\n", "NC_047559.1\t10920\t10922\n", "NC_047559.1\t10950\t10952\n", "NC_047559.1\t11000\t11002\n", "NC_047559.1\t11026\t11028\n", "NC_047559.1\t14214\t14216\n", "NC_047559.1\t14232\t14234\n", "NC_047559.1\t14243\t14245\n", "NC_047559.1\t14259\t14261\n", "NC_047559.1\t14319\t14321\n", "\n", "==> zr3644_14_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-exonUTR <==\n", "NC_047559.1\t418038\t418040\n", "NC_047559.1\t431124\t431126\n", "NC_047559.1\t571583\t571585\n", "NC_047559.1\t571838\t571840\n", "NC_047559.1\t571906\t571908\n", "NC_047559.1\t571929\t571931\n", "NC_047559.1\t572049\t572051\n", "NC_047559.1\t572153\t572155\n", "NC_047559.1\t572233\t572235\n", "NC_047559.1\t572332\t572334\n", "\n", "==> zr3644_14_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-exonUTR <==\n", "NC_047559.1\t204732\t204734\n", "NC_047559.1\t327844\t327846\n", "NC_047559.1\t545687\t545689\n", "NC_047559.1\t571793\t571795\n", "NC_047559.1\t572263\t572265\n", "NC_047559.1\t572453\t572455\n", "NC_047559.1\t572603\t572605\n", "NC_047559.1\t602021\t602023\n", "NC_047559.1\t617783\t617785\n", "NC_047559.1\t618187\t618189\n", "\n", "==> zr3644_14_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-exonUTR <==\n", "NC_047559.1\t10899\t10901\n", "NC_047559.1\t10920\t10922\n", "NC_047559.1\t10950\t10952\n", "NC_047559.1\t11000\t11002\n", "NC_047559.1\t11026\t11028\n", "NC_047559.1\t11080\t11082\n", "NC_047559.1\t14214\t14216\n", "NC_047559.1\t14232\t14234\n", "NC_047559.1\t14243\t14245\n", "NC_047559.1\t14259\t14261\n", "\n", "==> zr3644_15_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-exonUTR <==\n", "NC_047559.1\t431124\t431126\n", "NC_047559.1\t431205\t431207\n", "NC_047559.1\t544387\t544389\n", "NC_047559.1\t545229\t545231\n", "NC_047559.1\t545256\t545258\n", "NC_047559.1\t545687\t545689\n", "NC_047559.1\t571906\t571908\n", "NC_047559.1\t571929\t571931\n", "NC_047559.1\t572049\t572051\n", "NC_047559.1\t572075\t572077\n", "\n", "==> zr3644_15_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-exonUTR <==\n", "NC_047559.1\t19113\t19115\n", "NC_047559.1\t80380\t80382\n", "NC_047559.1\t343538\t343540\n", "NC_047559.1\t343574\t343576\n", "NC_047559.1\t544240\t544242\n", "NC_047559.1\t544307\t544309\n", "NC_047559.1\t544592\t544594\n", "NC_047559.1\t572153\t572155\n", "NC_047559.1\t572557\t572559\n", "NC_047559.1\t572569\t572571\n", "\n", "==> zr3644_15_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-exonUTR <==\n", "NC_047559.1\t10899\t10901\n", "NC_047559.1\t10920\t10922\n", "NC_047559.1\t10950\t10952\n", "NC_047559.1\t11000\t11002\n", "NC_047559.1\t11026\t11028\n", "NC_047559.1\t11080\t11082\n", "NC_047559.1\t14214\t14216\n", "NC_047559.1\t14232\t14234\n", "NC_047559.1\t14243\t14245\n", "NC_047559.1\t14259\t14261\n", "\n", "==> zr3644_16_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-exonUTR <==\n", "NC_047559.1\t431124\t431126\n", "NC_047559.1\t544592\t544594\n", "NC_047559.1\t544784\t544786\n", "NC_047559.1\t545687\t545689\n", "NC_047559.1\t571583\t571585\n", "NC_047559.1\t571838\t571840\n", "NC_047559.1\t571906\t571908\n", "NC_047559.1\t571929\t571931\n", "NC_047559.1\t572075\t572077\n", "NC_047559.1\t572153\t572155\n", "\n", "==> zr3644_16_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-exonUTR <==\n", "NC_047559.1\t19097\t19099\n", "NC_047559.1\t343479\t343481\n", "NC_047559.1\t343538\t343540\n", "NC_047559.1\t431205\t431207\n", "NC_047559.1\t544366\t544368\n", "NC_047559.1\t544552\t544554\n", "NC_047559.1\t545229\t545231\n", "NC_047559.1\t572332\t572334\n", "NC_047559.1\t572557\t572559\n", "NC_047559.1\t573040\t573042\n", "\n", "==> zr3644_16_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-exonUTR <==\n", "NC_047559.1\t10899\t10901\n", "NC_047559.1\t10920\t10922\n", "NC_047559.1\t10950\t10952\n", "NC_047559.1\t14214\t14216\n", "NC_047559.1\t14232\t14234\n", "NC_047559.1\t14243\t14245\n", "NC_047559.1\t14259\t14261\n", "NC_047559.1\t14319\t14321\n", "NC_047559.1\t14397\t14399\n", "NC_047559.1\t14401\t14403\n", "\n", "==> zr3644_17_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-exonUTR <==\n", "NC_047559.1\t431124\t431126\n", "NC_047559.1\t545229\t545231\n", "NC_047559.1\t571583\t571585\n", "NC_047559.1\t571793\t571795\n", "NC_047559.1\t571906\t571908\n", "NC_047559.1\t571929\t571931\n", "NC_047559.1\t572075\t572077\n", "NC_047559.1\t572153\t572155\n", "NC_047559.1\t572233\t572235\n", "NC_047559.1\t572245\t572247\n", "\n", "==> zr3644_17_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-exonUTR <==\n", "NC_047559.1\t85405\t85407\n", "NC_047559.1\t228335\t228337\n", "NC_047559.1\t343538\t343540\n", "NC_047559.1\t418038\t418040\n", "NC_047559.1\t544307\t544309\n", "NC_047559.1\t544552\t544554\n", "NC_047559.1\t545256\t545258\n", "NC_047559.1\t572263\t572265\n", "NC_047559.1\t572900\t572902\n", "NC_047559.1\t602057\t602059\n", "\n", "==> zr3644_17_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-exonUTR <==\n", "NC_047559.1\t10899\t10901\n", "NC_047559.1\t10920\t10922\n", "NC_047559.1\t10950\t10952\n", "NC_047559.1\t11000\t11002\n", "NC_047559.1\t11026\t11028\n", "NC_047559.1\t14214\t14216\n", "NC_047559.1\t14232\t14234\n", "NC_047559.1\t14243\t14245\n", "NC_047559.1\t14259\t14261\n", "NC_047559.1\t14319\t14321\n", "\n", "==> zr3644_18_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-exonUTR <==\n", "NC_047559.1\t431124\t431126\n", "NC_047559.1\t571583\t571585\n", "NC_047559.1\t571793\t571795\n", "NC_047559.1\t571838\t571840\n", "NC_047559.1\t571906\t571908\n", "NC_047559.1\t571929\t571931\n", "NC_047559.1\t572049\t572051\n", "NC_047559.1\t572075\t572077\n", "NC_047559.1\t572153\t572155\n", "NC_047559.1\t572233\t572235\n", "\n", "==> zr3644_18_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-exonUTR <==\n", "NC_047559.1\t11026\t11028\n", "NC_047559.1\t80380\t80382\n", "NC_047559.1\t242920\t242922\n", "NC_047559.1\t343676\t343678\n", "NC_047559.1\t415714\t415716\n", "NC_047559.1\t415739\t415741\n", "NC_047559.1\t415822\t415824\n", "NC_047559.1\t415957\t415959\n", "NC_047559.1\t415975\t415977\n", "NC_047559.1\t415988\t415990\n", "\n", "==> zr3644_18_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-exonUTR <==\n", "NC_047559.1\t10899\t10901\n", "NC_047559.1\t10920\t10922\n", "NC_047559.1\t10950\t10952\n", "NC_047559.1\t11000\t11002\n", "NC_047559.1\t11080\t11082\n", "NC_047559.1\t14214\t14216\n", "NC_047559.1\t14232\t14234\n", "NC_047559.1\t14243\t14245\n", "NC_047559.1\t14259\t14261\n", "NC_047559.1\t14319\t14321\n", "\n", "==> zr3644_19_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-exonUTR <==\n", "NC_047559.1\t431205\t431207\n", "NC_047559.1\t571838\t571840\n", "NC_047559.1\t571906\t571908\n", "NC_047559.1\t571929\t571931\n", "NC_047559.1\t572049\t572051\n", "NC_047559.1\t572075\t572077\n", "NC_047559.1\t572153\t572155\n", "NC_047559.1\t572233\t572235\n", "NC_047559.1\t572245\t572247\n", "NC_047559.1\t572332\t572334\n", "\n", "==> zr3644_19_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-exonUTR <==\n", "NC_047559.1\t11080\t11082\n", "NC_047559.1\t242485\t242487\n", "NC_047559.1\t431124\t431126\n", "NC_047559.1\t469758\t469760\n", "NC_047559.1\t473076\t473078\n", "NC_047559.1\t544552\t544554\n", "NC_047559.1\t544784\t544786\n", "NC_047559.1\t571793\t571795\n", "NC_047559.1\t572367\t572369\n", "NC_047559.1\t589456\t589458\n", "\n", "==> zr3644_19_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-exonUTR <==\n", "NC_047559.1\t10899\t10901\n", "NC_047559.1\t10920\t10922\n", "NC_047559.1\t10950\t10952\n", "NC_047559.1\t11000\t11002\n", "NC_047559.1\t11026\t11028\n", "NC_047559.1\t14214\t14216\n", "NC_047559.1\t14232\t14234\n", "NC_047559.1\t14243\t14245\n", "NC_047559.1\t14259\t14261\n", "NC_047559.1\t14319\t14321\n", "\n", "==> zr3644_1_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-exonUTR <==\n", "NC_047559.1\t571793\t571795\n", "NC_047559.1\t571838\t571840\n", "NC_047559.1\t571929\t571931\n", "NC_047559.1\t572233\t572235\n", "NC_047559.1\t572245\t572247\n", "NC_047559.1\t572263\t572265\n", "NC_047559.1\t572332\t572334\n", "NC_047559.1\t572453\t572455\n", "NC_047559.1\t572557\t572559\n", "NC_047559.1\t572569\t572571\n", "\n", "==> zr3644_1_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-exonUTR <==\n", "NC_047559.1\t477548\t477550\n", "NC_047559.1\t545229\t545231\n", "NC_047559.1\t571583\t571585\n", "NC_047559.1\t572153\t572155\n", "NC_047559.1\t572367\t572369\n", "NC_047559.1\t572900\t572902\n", "NC_047559.1\t596489\t596491\n", "NC_047559.1\t597401\t597403\n", "NC_047559.1\t601710\t601712\n", "NC_047559.1\t602021\t602023\n", "\n", "==> zr3644_1_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-exonUTR <==\n", "NC_047559.1\t10899\t10901\n", "NC_047559.1\t10920\t10922\n", "NC_047559.1\t10950\t10952\n", "NC_047559.1\t11000\t11002\n", "NC_047559.1\t11026\t11028\n", "NC_047559.1\t14214\t14216\n", "NC_047559.1\t14232\t14234\n", "NC_047559.1\t14243\t14245\n", "NC_047559.1\t14259\t14261\n", "NC_047559.1\t14319\t14321\n", "\n", "==> zr3644_20_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-exonUTR <==\n", "NC_047559.1\t431124\t431126\n", "NC_047559.1\t571583\t571585\n", "NC_047559.1\t571906\t571908\n", "NC_047559.1\t571929\t571931\n", "NC_047559.1\t572367\t572369\n", "NC_047559.1\t572453\t572455\n", "NC_047559.1\t572557\t572559\n", "NC_047559.1\t572569\t572571\n", "NC_047559.1\t572579\t572581\n", "NC_047559.1\t572603\t572605\n", "\n", "==> zr3644_20_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-exonUTR <==\n", "NC_047559.1\t14243\t14245\n", "NC_047559.1\t431205\t431207\n", "NC_047559.1\t544307\t544309\n", "NC_047559.1\t544552\t544554\n", "NC_047559.1\t544592\t544594\n", "NC_047559.1\t544784\t544786\n", "NC_047559.1\t545687\t545689\n", "NC_047559.1\t571793\t571795\n", "NC_047559.1\t572153\t572155\n", "NC_047559.1\t572332\t572334\n", "\n", "==> zr3644_20_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-exonUTR <==\n", "NC_047559.1\t10899\t10901\n", "NC_047559.1\t10920\t10922\n", "NC_047559.1\t10950\t10952\n", "NC_047559.1\t11000\t11002\n", "NC_047559.1\t11026\t11028\n", "NC_047559.1\t14214\t14216\n", "NC_047559.1\t14232\t14234\n", "NC_047559.1\t14259\t14261\n", "NC_047559.1\t14319\t14321\n", "NC_047559.1\t14397\t14399\n", "\n", "==> zr3644_21_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-exonUTR <==\n", "NC_047559.1\t431205\t431207\n", "NC_047559.1\t545687\t545689\n", "NC_047559.1\t571583\t571585\n", "NC_047559.1\t571793\t571795\n", "NC_047559.1\t571838\t571840\n", "NC_047559.1\t571906\t571908\n", "NC_047559.1\t571929\t571931\n", "NC_047559.1\t572049\t572051\n", "NC_047559.1\t572153\t572155\n", "NC_047559.1\t572233\t572235\n", "\n", "==> zr3644_21_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-exonUTR <==\n", "NC_047559.1\t337166\t337168\n", "NC_047559.1\t431124\t431126\n", "NC_047559.1\t544784\t544786\n", "NC_047559.1\t560388\t560390\n", "NC_047559.1\t572332\t572334\n", "NC_047559.1\t572367\t572369\n", "NC_047559.1\t572900\t572902\n", "NC_047559.1\t597401\t597403\n", "NC_047559.1\t601710\t601712\n", "NC_047559.1\t602021\t602023\n", "\n", "==> zr3644_21_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-exonUTR <==\n", "NC_047559.1\t10899\t10901\n", "NC_047559.1\t10920\t10922\n", "NC_047559.1\t10950\t10952\n", "NC_047559.1\t11000\t11002\n", "NC_047559.1\t11026\t11028\n", "NC_047559.1\t14214\t14216\n", "NC_047559.1\t14232\t14234\n", "NC_047559.1\t14243\t14245\n", "NC_047559.1\t14259\t14261\n", "NC_047559.1\t14319\t14321\n", "\n", "==> zr3644_22_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-exonUTR <==\n", "NC_047559.1\t544552\t544554\n", "NC_047559.1\t544592\t544594\n", "NC_047559.1\t545229\t545231\n", "NC_047559.1\t571583\t571585\n", "NC_047559.1\t571838\t571840\n", "NC_047559.1\t571906\t571908\n", "NC_047559.1\t571929\t571931\n", "NC_047559.1\t572049\t572051\n", "NC_047559.1\t572075\t572077\n", "NC_047559.1\t572453\t572455\n", "\n", "==> zr3644_22_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-exonUTR <==\n", "NC_047559.1\t11080\t11082\n", "NC_047559.1\t431124\t431126\n", "NC_047559.1\t453329\t453331\n", "NC_047559.1\t544784\t544786\n", "NC_047559.1\t545256\t545258\n", "NC_047559.1\t571793\t571795\n", "NC_047559.1\t572900\t572902\n", "NC_047559.1\t601710\t601712\n", "NC_047559.1\t602069\t602071\n", "NC_047559.1\t602281\t602283\n", "\n", "==> zr3644_22_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-exonUTR <==\n", "NC_047559.1\t10899\t10901\n", "NC_047559.1\t10920\t10922\n", "NC_047559.1\t10950\t10952\n", "NC_047559.1\t11000\t11002\n", "NC_047559.1\t11026\t11028\n", "NC_047559.1\t14214\t14216\n", "NC_047559.1\t14232\t14234\n", "NC_047559.1\t14243\t14245\n", "NC_047559.1\t14259\t14261\n", "NC_047559.1\t14319\t14321\n", "\n", "==> zr3644_23_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-exonUTR <==\n", "NC_047559.1\t431124\t431126\n", "NC_047559.1\t571793\t571795\n", "NC_047559.1\t571906\t571908\n", "NC_047559.1\t571929\t571931\n", "NC_047559.1\t572075\t572077\n", "NC_047559.1\t572233\t572235\n", "NC_047559.1\t572245\t572247\n", "NC_047559.1\t572332\t572334\n", "NC_047559.1\t572900\t572902\n", "NC_047559.1\t572952\t572954\n", "\n", "==> zr3644_23_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-exonUTR <==\n", "NC_047559.1\t473159\t473161\n", "NC_047559.1\t544387\t544389\n", "NC_047559.1\t544784\t544786\n", "NC_047559.1\t571583\t571585\n", "NC_047559.1\t572153\t572155\n", "NC_047559.1\t572263\t572265\n", "NC_047559.1\t596489\t596491\n", "NC_047559.1\t617783\t617785\n", "NC_047559.1\t618187\t618189\n", "NC_047559.1\t715028\t715030\n", "\n", "==> zr3644_23_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-exonUTR <==\n", "NC_047559.1\t10899\t10901\n", "NC_047559.1\t10920\t10922\n", "NC_047559.1\t10950\t10952\n", "NC_047559.1\t11000\t11002\n", "NC_047559.1\t11026\t11028\n", "NC_047559.1\t14214\t14216\n", "NC_047559.1\t14232\t14234\n", "NC_047559.1\t14243\t14245\n", "NC_047559.1\t14259\t14261\n", "NC_047559.1\t14319\t14321\n", "\n", "==> zr3644_24_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-exonUTR <==\n", "NC_047559.1\t431205\t431207\n", "NC_047559.1\t571583\t571585\n", "NC_047559.1\t571793\t571795\n", "NC_047559.1\t571838\t571840\n", "NC_047559.1\t571906\t571908\n", "NC_047559.1\t571929\t571931\n", "NC_047559.1\t572049\t572051\n", "NC_047559.1\t572075\t572077\n", "NC_047559.1\t572153\t572155\n", "NC_047559.1\t572245\t572247\n", "\n", "==> zr3644_24_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-exonUTR <==\n", "NC_047559.1\t10950\t10952\n", "NC_047559.1\t19105\t19107\n", "NC_047559.1\t19113\t19115\n", "NC_047559.1\t19119\t19121\n", "NC_047559.1\t343479\t343481\n", "NC_047559.1\t343538\t343540\n", "NC_047559.1\t416078\t416080\n", "NC_047559.1\t431124\t431126\n", "NC_047559.1\t473159\t473161\n", "NC_047559.1\t572332\t572334\n", "\n", "==> zr3644_24_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-exonUTR <==\n", "NC_047559.1\t10899\t10901\n", "NC_047559.1\t10920\t10922\n", "NC_047559.1\t11000\t11002\n", "NC_047559.1\t11026\t11028\n", "NC_047559.1\t14214\t14216\n", "NC_047559.1\t14232\t14234\n", "NC_047559.1\t14243\t14245\n", "NC_047559.1\t14259\t14261\n", "NC_047559.1\t14319\t14321\n", "NC_047559.1\t14397\t14399\n", "\n", "==> zr3644_2_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-exonUTR <==\n", "NC_047559.1\t431124\t431126\n", "NC_047559.1\t544387\t544389\n", "NC_047559.1\t544552\t544554\n", "NC_047559.1\t571793\t571795\n", "NC_047559.1\t571838\t571840\n", "NC_047559.1\t571906\t571908\n", "NC_047559.1\t571929\t571931\n", "NC_047559.1\t572049\t572051\n", "NC_047559.1\t572075\t572077\n", "NC_047559.1\t572233\t572235\n", "\n", "==> zr3644_2_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-exonUTR <==\n", "NC_047559.1\t11026\t11028\n", "NC_047559.1\t19113\t19115\n", "NC_047559.1\t343479\t343481\n", "NC_047559.1\t343574\t343576\n", "NC_047559.1\t343603\t343605\n", "NC_047559.1\t424199\t424201\n", "NC_047559.1\t540317\t540319\n", "NC_047559.1\t544307\t544309\n", "NC_047559.1\t544533\t544535\n", "NC_047559.1\t545229\t545231\n", "\n", "==> zr3644_2_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-exonUTR <==\n", "NC_047559.1\t10899\t10901\n", "NC_047559.1\t10920\t10922\n", "NC_047559.1\t10950\t10952\n", "NC_047559.1\t11000\t11002\n", "NC_047559.1\t14214\t14216\n", "NC_047559.1\t14232\t14234\n", "NC_047559.1\t14243\t14245\n", "NC_047559.1\t14259\t14261\n", "NC_047559.1\t14319\t14321\n", "NC_047559.1\t14397\t14399\n", "\n", "==> zr3644_3_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-exonUTR <==\n", "NC_047559.1\t415945\t415947\n", "NC_047559.1\t415957\t415959\n", "NC_047559.1\t415975\t415977\n", "NC_047559.1\t415988\t415990\n", "NC_047559.1\t415998\t416000\n", "NC_047559.1\t571583\t571585\n", "NC_047559.1\t571838\t571840\n", "NC_047559.1\t571906\t571908\n", "NC_047559.1\t571929\t571931\n", "NC_047559.1\t572049\t572051\n", "\n", "==> zr3644_3_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-exonUTR <==\n", "NC_047559.1\t431124\t431126\n", "NC_047559.1\t431205\t431207\n", "NC_047559.1\t453629\t453631\n", "NC_047559.1\t473159\t473161\n", "NC_047559.1\t544366\t544368\n", "NC_047559.1\t544387\t544389\n", "NC_047559.1\t544784\t544786\n", "NC_047559.1\t545229\t545231\n", "NC_047559.1\t545256\t545258\n", "NC_047559.1\t571793\t571795\n", "\n", "==> zr3644_3_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-exonUTR <==\n", "NC_047559.1\t10899\t10901\n", "NC_047559.1\t10920\t10922\n", "NC_047559.1\t10950\t10952\n", "NC_047559.1\t11000\t11002\n", "NC_047559.1\t11026\t11028\n", "NC_047559.1\t14214\t14216\n", "NC_047559.1\t14232\t14234\n", "NC_047559.1\t14243\t14245\n", "NC_047559.1\t14259\t14261\n", "NC_047559.1\t14319\t14321\n", "\n", "==> zr3644_4_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-exonUTR <==\n", "NC_047559.1\t415822\t415824\n", "NC_047559.1\t415998\t416000\n", "NC_047559.1\t544366\t544368\n", "NC_047559.1\t544533\t544535\n", "NC_047559.1\t544552\t544554\n", "NC_047559.1\t545687\t545689\n", "NC_047559.1\t571583\t571585\n", "NC_047559.1\t571906\t571908\n", "NC_047559.1\t571929\t571931\n", "NC_047559.1\t572332\t572334\n", "\n", "==> zr3644_4_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-exonUTR <==\n", "NC_047559.1\t431205\t431207\n", "NC_047559.1\t544387\t544389\n", "NC_047559.1\t544404\t544406\n", "NC_047559.1\t544784\t544786\n", "NC_047559.1\t572049\t572051\n", "NC_047559.1\t596489\t596491\n", "NC_047559.1\t596496\t596498\n", "NC_047559.1\t617783\t617785\n", "NC_047559.1\t618187\t618189\n", "NC_047559.1\t632593\t632595\n", "\n", "==> zr3644_4_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-exonUTR <==\n", "NC_047559.1\t10899\t10901\n", "NC_047559.1\t10920\t10922\n", "NC_047559.1\t10950\t10952\n", "NC_047559.1\t11000\t11002\n", "NC_047559.1\t11026\t11028\n", "NC_047559.1\t14214\t14216\n", "NC_047559.1\t14232\t14234\n", "NC_047559.1\t14243\t14245\n", "NC_047559.1\t14259\t14261\n", "NC_047559.1\t14319\t14321\n", "\n", "==> zr3644_5_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-exonUTR <==\n", "NC_047559.1\t431124\t431126\n", "NC_047559.1\t544552\t544554\n", "NC_047559.1\t544592\t544594\n", "NC_047559.1\t545687\t545689\n", "NC_047559.1\t571583\t571585\n", "NC_047559.1\t571838\t571840\n", "NC_047559.1\t571906\t571908\n", "NC_047559.1\t571929\t571931\n", "NC_047559.1\t572075\t572077\n", "NC_047559.1\t572332\t572334\n", "\n", "==> zr3644_5_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-exonUTR <==\n", "NC_047559.1\t19113\t19115\n", "NC_047559.1\t145413\t145415\n", "NC_047559.1\t145416\t145418\n", "NC_047559.1\t145421\t145423\n", "NC_047559.1\t145424\t145426\n", "NC_047559.1\t145430\t145432\n", "NC_047559.1\t327768\t327770\n", "NC_047559.1\t431205\t431207\n", "NC_047559.1\t453602\t453604\n", "NC_047559.1\t458881\t458883\n", "\n", "==> zr3644_5_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-exonUTR <==\n", "NC_047559.1\t10899\t10901\n", "NC_047559.1\t10920\t10922\n", "NC_047559.1\t10950\t10952\n", "NC_047559.1\t11000\t11002\n", "NC_047559.1\t11026\t11028\n", "NC_047559.1\t11080\t11082\n", "NC_047559.1\t14214\t14216\n", "NC_047559.1\t14232\t14234\n", "NC_047559.1\t14243\t14245\n", "NC_047559.1\t14259\t14261\n", "\n", "==> zr3644_6_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-exonUTR <==\n", "NC_047559.1\t544784\t544786\n", "NC_047559.1\t545256\t545258\n", "NC_047559.1\t545687\t545689\n", "NC_047559.1\t571583\t571585\n", "NC_047559.1\t571838\t571840\n", "NC_047559.1\t571906\t571908\n", "NC_047559.1\t571929\t571931\n", "NC_047559.1\t572049\t572051\n", "NC_047559.1\t572075\t572077\n", "NC_047559.1\t572153\t572155\n", "\n", "==> zr3644_6_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-exonUTR <==\n", "NC_047559.1\t19097\t19099\n", "NC_047559.1\t337166\t337168\n", "NC_047559.1\t343538\t343540\n", "NC_047559.1\t431124\t431126\n", "NC_047559.1\t431205\t431207\n", "NC_047559.1\t469384\t469386\n", "NC_047559.1\t544366\t544368\n", "NC_047559.1\t544387\t544389\n", "NC_047559.1\t571793\t571795\n", "NC_047559.1\t602021\t602023\n", "\n", "==> zr3644_6_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-exonUTR <==\n", "NC_047559.1\t10899\t10901\n", "NC_047559.1\t10920\t10922\n", "NC_047559.1\t10950\t10952\n", "NC_047559.1\t11000\t11002\n", "NC_047559.1\t11026\t11028\n", "NC_047559.1\t14214\t14216\n", "NC_047559.1\t14232\t14234\n", "NC_047559.1\t14243\t14245\n", "NC_047559.1\t14259\t14261\n", "NC_047559.1\t14319\t14321\n", "\n", "==> zr3644_7_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-exonUTR <==\n", "NC_047559.1\t415945\t415947\n", "NC_047559.1\t415957\t415959\n", "NC_047559.1\t415975\t415977\n", "NC_047559.1\t415998\t416000\n", "NC_047559.1\t416071\t416073\n", "NC_047559.1\t416088\t416090\n", "NC_047559.1\t431124\t431126\n", "NC_047559.1\t431205\t431207\n", "NC_047559.1\t544387\t544389\n", "NC_047559.1\t544404\t544406\n", "\n", "==> zr3644_7_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-exonUTR <==\n", "NC_047559.1\t19083\t19085\n", "NC_047559.1\t19097\t19099\n", "NC_047559.1\t19105\t19107\n", "NC_047559.1\t126263\t126265\n", "NC_047559.1\t337166\t337168\n", "NC_047559.1\t343538\t343540\n", "NC_047559.1\t343574\t343576\n", "NC_047559.1\t343603\t343605\n", "NC_047559.1\t343655\t343657\n", "NC_047559.1\t415988\t415990\n", "\n", "==> zr3644_7_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-exonUTR <==\n", "NC_047559.1\t10899\t10901\n", "NC_047559.1\t10920\t10922\n", "NC_047559.1\t10950\t10952\n", "NC_047559.1\t11000\t11002\n", "NC_047559.1\t11026\t11028\n", "NC_047559.1\t14214\t14216\n", "NC_047559.1\t14232\t14234\n", "NC_047559.1\t14243\t14245\n", "NC_047559.1\t14259\t14261\n", "NC_047559.1\t14319\t14321\n", "\n", "==> zr3644_8_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-exonUTR <==\n", "NC_047559.1\t431205\t431207\n", "NC_047559.1\t544387\t544389\n", "NC_047559.1\t571583\t571585\n", "NC_047559.1\t571793\t571795\n", "NC_047559.1\t571906\t571908\n", "NC_047559.1\t571929\t571931\n", "NC_047559.1\t572153\t572155\n", "NC_047559.1\t572233\t572235\n", "NC_047559.1\t572557\t572559\n", "NC_047559.1\t572569\t572571\n", "\n", "==> zr3644_8_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-exonUTR <==\n", "NC_047559.1\t19097\t19099\n", "NC_047559.1\t19105\t19107\n", "NC_047559.1\t19113\t19115\n", "NC_047559.1\t19119\t19121\n", "NC_047559.1\t209689\t209691\n", "NC_047559.1\t337166\t337168\n", "NC_047559.1\t473159\t473161\n", "NC_047559.1\t540078\t540080\n", "NC_047559.1\t544307\t544309\n", "NC_047559.1\t544592\t544594\n", "\n", "==> zr3644_8_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-exonUTR <==\n", "NC_047559.1\t10899\t10901\n", "NC_047559.1\t10920\t10922\n", "NC_047559.1\t10950\t10952\n", "NC_047559.1\t11000\t11002\n", "NC_047559.1\t11026\t11028\n", "NC_047559.1\t11080\t11082\n", "NC_047559.1\t14214\t14216\n", "NC_047559.1\t14232\t14234\n", "NC_047559.1\t14243\t14245\n", "NC_047559.1\t14259\t14261\n", "\n", "==> zr3644_9_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-exonUTR <==\n", "NC_047559.1\t431124\t431126\n", "NC_047559.1\t431205\t431207\n", "NC_047559.1\t544592\t544594\n", "NC_047559.1\t545687\t545689\n", "NC_047559.1\t571906\t571908\n", "NC_047559.1\t571929\t571931\n", "NC_047559.1\t572049\t572051\n", "NC_047559.1\t572075\t572077\n", "NC_047559.1\t572153\t572155\n", "NC_047559.1\t572453\t572455\n", "\n", "==> zr3644_9_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-exonUTR <==\n", "NC_047559.1\t544387\t544389\n", "NC_047559.1\t544533\t544535\n", "NC_047559.1\t597401\t597403\n", "NC_047559.1\t601710\t601712\n", "NC_047559.1\t617978\t617980\n", "NC_047559.1\t715002\t715004\n", "NC_047559.1\t715028\t715030\n", "NC_047559.1\t715048\t715050\n", "NC_047559.1\t748271\t748273\n", "NC_047559.1\t748282\t748284\n", "\n", "==> zr3644_9_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-exonUTR <==\n", "NC_047559.1\t10899\t10901\n", "NC_047559.1\t10920\t10922\n", "NC_047559.1\t10950\t10952\n", "NC_047559.1\t11000\t11002\n", "NC_047559.1\t14214\t14216\n", "NC_047559.1\t14232\t14234\n", "NC_047559.1\t14243\t14245\n", "NC_047559.1\t14259\t14261\n", "NC_047559.1\t14319\t14321\n", "NC_047559.1\t14397\t14399\n", "\n", "==> zr3644_union-averages_5x.bedgraph-Meth.bed-exonUTR <==\n", "NC_047559.1\t571583\t571585\n", "NC_047559.1\t571838\t571840\n", "NC_047559.1\t571906\t571908\n", "NC_047559.1\t571929\t571931\n", "NC_047559.1\t572049\t572051\n", "NC_047559.1\t572075\t572077\n", "NC_047559.1\t572153\t572155\n", "NC_047559.1\t572233\t572235\n", "NC_047559.1\t572245\t572247\n", "NC_047559.1\t572263\t572265\n", "\n", "==> zr3644_union-averages_5x.bedgraph-sparseMeth.bed-exonUTR <==\n", "NC_047559.1\t145413\t145415\n", "NC_047559.1\t145416\t145418\n", "NC_047559.1\t145421\t145423\n", "NC_047559.1\t145424\t145426\n", "NC_047559.1\t145430\t145432\n", "NC_047559.1\t415714\t415716\n", "NC_047559.1\t415739\t415741\n", "NC_047559.1\t415822\t415824\n", "NC_047559.1\t415945\t415947\n", "NC_047559.1\t415957\t415959\n", "\n", "==> zr3644_union-averages_5x.bedgraph-unMeth.bed-exonUTR <==\n", "NC_047559.1\t10899\t10901\n", "NC_047559.1\t10920\t10922\n", "NC_047559.1\t10950\t10952\n", "NC_047559.1\t11000\t11002\n", "NC_047559.1\t11026\t11028\n", "NC_047559.1\t11080\t11082\n", "NC_047559.1\t14214\t14216\n", "NC_047559.1\t14232\t14234\n", "NC_047559.1\t14243\t14245\n", "NC_047559.1\t14259\t14261\n" ] } ], "source": [ "#Check output\n", "!head *exonUTR" ] }, { "cell_type": "code", "execution_count": 49, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ " 41929 zr3644_10_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-exonUTR\n", " 30046 zr3644_10_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-exonUTR\n", " 366136 zr3644_10_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-exonUTR\n", " 42629 zr3644_11_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-exonUTR\n", " 31927 zr3644_11_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-exonUTR\n", " 379558 zr3644_11_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-exonUTR\n", " 39179 zr3644_12_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-exonUTR\n", " 30144 zr3644_12_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-exonUTR\n", " 355660 zr3644_12_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-exonUTR\n", " 42282 zr3644_13_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-exonUTR\n", " 33224 zr3644_13_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-exonUTR\n", " 375672 zr3644_13_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-exonUTR\n", " 40952 zr3644_14_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-exonUTR\n", " 21101 zr3644_14_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-exonUTR\n", " 304345 zr3644_14_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-exonUTR\n", " 48836 zr3644_15_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-exonUTR\n", " 34037 zr3644_15_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-exonUTR\n", " 381649 zr3644_15_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-exonUTR\n", " 38539 zr3644_16_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-exonUTR\n", " 29285 zr3644_16_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-exonUTR\n", " 350951 zr3644_16_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-exonUTR\n", " 41396 zr3644_17_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-exonUTR\n", " 27053 zr3644_17_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-exonUTR\n", " 374638 zr3644_17_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-exonUTR\n", " 39217 zr3644_18_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-exonUTR\n", " 30982 zr3644_18_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-exonUTR\n", " 362617 zr3644_18_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-exonUTR\n", " 38436 zr3644_19_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-exonUTR\n", " 29469 zr3644_19_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-exonUTR\n", " 360717 zr3644_19_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-exonUTR\n", " 33160 zr3644_1_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-exonUTR\n", " 31718 zr3644_1_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-exonUTR\n", " 354480 zr3644_1_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-exonUTR\n", " 40545 zr3644_20_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-exonUTR\n", " 32043 zr3644_20_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-exonUTR\n", " 372705 zr3644_20_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-exonUTR\n", " 40513 zr3644_21_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-exonUTR\n", " 32477 zr3644_21_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-exonUTR\n", " 368435 zr3644_21_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-exonUTR\n", " 37597 zr3644_22_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-exonUTR\n", " 28841 zr3644_22_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-exonUTR\n", " 351693 zr3644_22_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-exonUTR\n", " 33318 zr3644_23_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-exonUTR\n", " 26442 zr3644_23_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-exonUTR\n", " 321068 zr3644_23_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-exonUTR\n", " 39736 zr3644_24_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-exonUTR\n", " 30780 zr3644_24_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-exonUTR\n", " 367256 zr3644_24_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-exonUTR\n", " 42050 zr3644_2_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-exonUTR\n", " 27270 zr3644_2_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-exonUTR\n", " 381068 zr3644_2_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-exonUTR\n", " 34375 zr3644_3_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-exonUTR\n", " 27500 zr3644_3_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-exonUTR\n", " 322341 zr3644_3_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-exonUTR\n", " 39355 zr3644_4_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-exonUTR\n", " 29881 zr3644_4_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-exonUTR\n", " 362622 zr3644_4_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-exonUTR\n", " 36976 zr3644_5_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-exonUTR\n", " 29278 zr3644_5_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-exonUTR\n", " 345943 zr3644_5_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-exonUTR\n", " 40993 zr3644_6_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-exonUTR\n", " 31337 zr3644_6_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-exonUTR\n", " 373618 zr3644_6_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-exonUTR\n", " 49756 zr3644_7_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-exonUTR\n", " 35621 zr3644_7_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-exonUTR\n", " 429289 zr3644_7_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-exonUTR\n", " 36528 zr3644_8_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-exonUTR\n", " 27903 zr3644_8_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-exonUTR\n", " 332713 zr3644_8_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-exonUTR\n", " 36569 zr3644_9_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-exonUTR\n", " 29113 zr3644_9_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-exonUTR\n", " 332600 zr3644_9_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-exonUTR\n", " 55067 zr3644_union-averages_5x.bedgraph-Meth.bed-exonUTR\n", " 46053 zr3644_union-averages_5x.bedgraph-sparseMeth.bed-exonUTR\n", " 507525 zr3644_union-averages_5x.bedgraph-unMeth.bed-exonUTR\n", " 10908757 total\n" ] } ], "source": [ "#Count number of overlaps\n", "!wc -l *exonUTR" ] }, { "cell_type": "code", "execution_count": 50, "metadata": { "collapsed": true }, "outputs": [], "source": [ "#Get line counts for each fine\n", "# Remove 28th line (total entries)\n", "#Ensure output is tab-delimited\n", "#Save output\n", "!wc -l *-exonUTR \\\n", "| sed '76,$ d' \\\n", "| awk '{print $1\"\\t\"$2}' \\\n", "> zr3644_5x-exonUTR-counts.txt" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "### 6e. Intron" ] }, { "cell_type": "code", "execution_count": 51, "metadata": { "collapsed": false }, "outputs": [], "source": [ "%%bash\n", "for f in *bed\n", "do\n", " /Users/Shared/bioinformatics/bedtools2/bin/intersectBed \\\n", " -u \\\n", " -a ${f} \\\n", " -b /Volumes/web-1/halfshell/genomic-databank/cgigas_uk_roslin_v1_intron.bed \\\n", " > ${f}-intron\n", "done" ] }, { "cell_type": "code", "execution_count": 52, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "==> zr3644_10_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-intron <==\n", "NC_047559.1\t356335\t356337\n", "NC_047559.1\t356436\t356438\n", "NC_047559.1\t356685\t356687\n", "NC_047559.1\t357799\t357801\n", "NC_047559.1\t357900\t357902\n", "NC_047559.1\t357955\t357957\n", "NC_047559.1\t358313\t358315\n", "NC_047559.1\t362609\t362611\n", "NC_047559.1\t416920\t416922\n", "NC_047559.1\t418551\t418553\n", "\n", "==> zr3644_10_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-intron <==\n", "NC_047559.1\t10270\t10272\n", "NC_047559.1\t10292\t10294\n", "NC_047559.1\t10358\t10360\n", "NC_047559.1\t18257\t18259\n", "NC_047559.1\t61081\t61083\n", "NC_047559.1\t62770\t62772\n", "NC_047559.1\t68070\t68072\n", "NC_047559.1\t72245\t72247\n", "NC_047559.1\t81263\t81265\n", "NC_047559.1\t100249\t100251\n", "\n", "==> zr3644_10_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-intron <==\n", "NC_047559.1\t10314\t10316\n", "NC_047559.1\t10845\t10847\n", "NC_047559.1\t10859\t10861\n", "NC_047559.1\t14770\t14772\n", "NC_047559.1\t14790\t14792\n", "NC_047559.1\t15481\t15483\n", "NC_047559.1\t15489\t15491\n", "NC_047559.1\t15538\t15540\n", "NC_047559.1\t18064\t18066\n", "NC_047559.1\t18078\t18080\n", "\n", "==> zr3644_11_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-intron <==\n", "NC_047559.1\t154324\t154326\n", "NC_047559.1\t356685\t356687\n", "NC_047559.1\t356699\t356701\n", "NC_047559.1\t356748\t356750\n", "NC_047559.1\t356910\t356912\n", "NC_047559.1\t356933\t356935\n", "NC_047559.1\t357501\t357503\n", "NC_047559.1\t357519\t357521\n", "NC_047559.1\t358313\t358315\n", "NC_047559.1\t358586\t358588\n", "\n", "==> zr3644_11_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-intron <==\n", "NC_047559.1\t61203\t61205\n", "NC_047559.1\t62770\t62772\n", "NC_047559.1\t68070\t68072\n", "NC_047559.1\t100154\t100156\n", "NC_047559.1\t153777\t153779\n", "NC_047559.1\t153815\t153817\n", "NC_047559.1\t153840\t153842\n", "NC_047559.1\t153850\t153852\n", "NC_047559.1\t153860\t153862\n", "NC_047559.1\t153864\t153866\n", "\n", "==> zr3644_11_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-intron <==\n", "NC_047559.1\t10155\t10157\n", "NC_047559.1\t10215\t10217\n", "NC_047559.1\t10270\t10272\n", "NC_047559.1\t10292\t10294\n", "NC_047559.1\t10314\t10316\n", "NC_047559.1\t10358\t10360\n", "NC_047559.1\t10402\t10404\n", "NC_047559.1\t10413\t10415\n", "NC_047559.1\t10457\t10459\n", "NC_047559.1\t10479\t10481\n", "\n", "==> zr3644_12_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-intron <==\n", "NC_047559.1\t424694\t424696\n", "NC_047559.1\t424941\t424943\n", "NC_047559.1\t425000\t425002\n", "NC_047559.1\t425018\t425020\n", "NC_047559.1\t425106\t425108\n", "NC_047559.1\t425124\t425126\n", "NC_047559.1\t425144\t425146\n", "NC_047559.1\t425159\t425161\n", "NC_047559.1\t425403\t425405\n", "NC_047559.1\t425491\t425493\n", "\n", "==> zr3644_12_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-intron <==\n", "NC_047559.1\t10358\t10360\n", "NC_047559.1\t10772\t10774\n", "NC_047559.1\t61081\t61083\n", "NC_047559.1\t62770\t62772\n", "NC_047559.1\t100180\t100182\n", "NC_047559.1\t153815\t153817\n", "NC_047559.1\t153830\t153832\n", "NC_047559.1\t153840\t153842\n", "NC_047559.1\t153850\t153852\n", "NC_047559.1\t153860\t153862\n", "\n", "==> zr3644_12_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-intron <==\n", "NC_047559.1\t10215\t10217\n", "NC_047559.1\t10270\t10272\n", "NC_047559.1\t10292\t10294\n", "NC_047559.1\t10314\t10316\n", "NC_047559.1\t10402\t10404\n", "NC_047559.1\t10413\t10415\n", "NC_047559.1\t10457\t10459\n", "NC_047559.1\t10479\t10481\n", "NC_047559.1\t10501\t10503\n", "NC_047559.1\t10545\t10547\n", "\n", "==> zr3644_13_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-intron <==\n", "NC_047559.1\t356335\t356337\n", "NC_047559.1\t356748\t356750\n", "NC_047559.1\t357501\t357503\n", "NC_047559.1\t357519\t357521\n", "NC_047559.1\t357784\t357786\n", "NC_047559.1\t357799\t357801\n", "NC_047559.1\t357900\t357902\n", "NC_047559.1\t357955\t357957\n", "NC_047559.1\t358043\t358045\n", "NC_047559.1\t359664\t359666\n", "\n", "==> zr3644_13_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-intron <==\n", "NC_047559.1\t10270\t10272\n", "NC_047559.1\t62770\t62772\n", "NC_047559.1\t68070\t68072\n", "NC_047559.1\t100180\t100182\n", "NC_047559.1\t100276\t100278\n", "NC_047559.1\t111728\t111730\n", "NC_047559.1\t113151\t113153\n", "NC_047559.1\t159869\t159871\n", "NC_047559.1\t160058\t160060\n", "NC_047559.1\t164025\t164027\n", "\n", "==> zr3644_13_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-intron <==\n", "NC_047559.1\t10292\t10294\n", "NC_047559.1\t10314\t10316\n", "NC_047559.1\t10358\t10360\n", "NC_047559.1\t10479\t10481\n", "NC_047559.1\t10501\t10503\n", "NC_047559.1\t10545\t10547\n", "NC_047559.1\t10547\t10549\n", "NC_047559.1\t10567\t10569\n", "NC_047559.1\t10772\t10774\n", "NC_047559.1\t10845\t10847\n", "\n", "==> zr3644_14_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-intron <==\n", "NC_047559.1\t62770\t62772\n", "NC_047559.1\t68070\t68072\n", "NC_047559.1\t164604\t164606\n", "NC_047559.1\t164626\t164628\n", "NC_047559.1\t164628\t164630\n", "NC_047559.1\t164642\t164644\n", "NC_047559.1\t164647\t164649\n", "NC_047559.1\t164662\t164664\n", "NC_047559.1\t375360\t375362\n", "NC_047559.1\t377621\t377623\n", "\n", "==> zr3644_14_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-intron <==\n", "NC_047559.1\t10457\t10459\n", "NC_047559.1\t60430\t60432\n", "NC_047559.1\t61081\t61083\n", "NC_047559.1\t61203\t61205\n", "NC_047559.1\t116738\t116740\n", "NC_047559.1\t161452\t161454\n", "NC_047559.1\t161468\t161470\n", "NC_047559.1\t161483\t161485\n", "NC_047559.1\t162988\t162990\n", "NC_047559.1\t163026\t163028\n", "\n", "==> zr3644_14_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-intron <==\n", "NC_047559.1\t10270\t10272\n", "NC_047559.1\t10292\t10294\n", "NC_047559.1\t10314\t10316\n", "NC_047559.1\t10358\t10360\n", "NC_047559.1\t10391\t10393\n", "NC_047559.1\t10402\t10404\n", "NC_047559.1\t10413\t10415\n", "NC_047559.1\t10479\t10481\n", "NC_047559.1\t10545\t10547\n", "NC_047559.1\t10612\t10614\n", "\n", "==> zr3644_15_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-intron <==\n", "NC_047559.1\t356335\t356337\n", "NC_047559.1\t356395\t356397\n", "NC_047559.1\t356430\t356432\n", "NC_047559.1\t356436\t356438\n", "NC_047559.1\t357955\t357957\n", "NC_047559.1\t357968\t357970\n", "NC_047559.1\t358017\t358019\n", "NC_047559.1\t358313\t358315\n", "NC_047559.1\t362609\t362611\n", "NC_047559.1\t380569\t380571\n", "\n", "==> zr3644_15_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-intron <==\n", "NC_047559.1\t10215\t10217\n", "NC_047559.1\t82007\t82009\n", "NC_047559.1\t83035\t83037\n", "NC_047559.1\t84068\t84070\n", "NC_047559.1\t100440\t100442\n", "NC_047559.1\t100964\t100966\n", "NC_047559.1\t107909\t107911\n", "NC_047559.1\t111760\t111762\n", "NC_047559.1\t159410\t159412\n", "NC_047559.1\t161226\t161228\n", "\n", "==> zr3644_15_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-intron <==\n", "NC_047559.1\t10155\t10157\n", "NC_047559.1\t10270\t10272\n", "NC_047559.1\t10292\t10294\n", "NC_047559.1\t10314\t10316\n", "NC_047559.1\t10358\t10360\n", "NC_047559.1\t10391\t10393\n", "NC_047559.1\t10457\t10459\n", "NC_047559.1\t10479\t10481\n", "NC_047559.1\t10501\t10503\n", "NC_047559.1\t10545\t10547\n", "\n", "==> zr3644_16_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-intron <==\n", "NC_047559.1\t356395\t356397\n", "NC_047559.1\t356430\t356432\n", "NC_047559.1\t357784\t357786\n", "NC_047559.1\t358527\t358529\n", "NC_047559.1\t358586\t358588\n", "NC_047559.1\t359671\t359673\n", "NC_047559.1\t359701\t359703\n", "NC_047559.1\t377621\t377623\n", "NC_047559.1\t377790\t377792\n", "NC_047559.1\t419606\t419608\n", "\n", "==> zr3644_16_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-intron <==\n", "NC_047559.1\t62770\t62772\n", "NC_047559.1\t154324\t154326\n", "NC_047559.1\t169393\t169395\n", "NC_047559.1\t169415\t169417\n", "NC_047559.1\t169433\t169435\n", "NC_047559.1\t169463\t169465\n", "NC_047559.1\t356335\t356337\n", "NC_047559.1\t356378\t356380\n", "NC_047559.1\t356436\t356438\n", "NC_047559.1\t357362\t357364\n", "\n", "==> zr3644_16_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-intron <==\n", "NC_047559.1\t10845\t10847\n", "NC_047559.1\t10859\t10861\n", "NC_047559.1\t14770\t14772\n", "NC_047559.1\t14790\t14792\n", "NC_047559.1\t15481\t15483\n", "NC_047559.1\t15489\t15491\n", "NC_047559.1\t15538\t15540\n", "NC_047559.1\t18064\t18066\n", "NC_047559.1\t18078\t18080\n", "NC_047559.1\t18152\t18154\n", "\n", "==> zr3644_17_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-intron <==\n", "NC_047559.1\t359671\t359673\n", "NC_047559.1\t359678\t359680\n", "NC_047559.1\t359701\t359703\n", "NC_047559.1\t360322\t360324\n", "NC_047559.1\t360361\t360363\n", "NC_047559.1\t360443\t360445\n", "NC_047559.1\t360640\t360642\n", "NC_047559.1\t361152\t361154\n", "NC_047559.1\t377961\t377963\n", "NC_047559.1\t416920\t416922\n", "\n", "==> zr3644_17_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-intron <==\n", "NC_047559.1\t18064\t18066\n", "NC_047559.1\t18078\t18080\n", "NC_047559.1\t18332\t18334\n", "NC_047559.1\t68070\t68072\n", "NC_047559.1\t68140\t68142\n", "NC_047559.1\t82158\t82160\n", "NC_047559.1\t115136\t115138\n", "NC_047559.1\t125225\t125227\n", "NC_047559.1\t161468\t161470\n", "NC_047559.1\t161483\t161485\n", "\n", "==> zr3644_17_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-intron <==\n", "NC_047559.1\t10380\t10382\n", "NC_047559.1\t10391\t10393\n", "NC_047559.1\t10402\t10404\n", "NC_047559.1\t10413\t10415\n", "NC_047559.1\t10457\t10459\n", "NC_047559.1\t10479\t10481\n", "NC_047559.1\t10501\t10503\n", "NC_047559.1\t10545\t10547\n", "NC_047559.1\t10547\t10549\n", "NC_047559.1\t10567\t10569\n", "\n", "==> zr3644_18_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-intron <==\n", "NC_047559.1\t356910\t356912\n", "NC_047559.1\t356933\t356935\n", "NC_047559.1\t359671\t359673\n", "NC_047559.1\t360322\t360324\n", "NC_047559.1\t360361\t360363\n", "NC_047559.1\t416920\t416922\n", "NC_047559.1\t418672\t418674\n", "NC_047559.1\t424941\t424943\n", "NC_047559.1\t425000\t425002\n", "NC_047559.1\t425018\t425020\n", "\n", "==> zr3644_18_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-intron <==\n", "NC_047559.1\t10358\t10360\n", "NC_047559.1\t18152\t18154\n", "NC_047559.1\t82357\t82359\n", "NC_047559.1\t82835\t82837\n", "NC_047559.1\t100154\t100156\n", "NC_047559.1\t100276\t100278\n", "NC_047559.1\t100305\t100307\n", "NC_047559.1\t113151\t113153\n", "NC_047559.1\t125921\t125923\n", "NC_047559.1\t154324\t154326\n", "\n", "==> zr3644_18_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-intron <==\n", "NC_047559.1\t10270\t10272\n", "NC_047559.1\t10292\t10294\n", "NC_047559.1\t10314\t10316\n", "NC_047559.1\t10380\t10382\n", "NC_047559.1\t10391\t10393\n", "NC_047559.1\t10402\t10404\n", "NC_047559.1\t10413\t10415\n", "NC_047559.1\t10457\t10459\n", "NC_047559.1\t10479\t10481\n", "NC_047559.1\t10501\t10503\n", "\n", "==> zr3644_19_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-intron <==\n", "NC_047559.1\t356335\t356337\n", "NC_047559.1\t356430\t356432\n", "NC_047559.1\t356436\t356438\n", "NC_047559.1\t356699\t356701\n", "NC_047559.1\t357362\t357364\n", "NC_047559.1\t357519\t357521\n", "NC_047559.1\t357751\t357753\n", "NC_047559.1\t357784\t357786\n", "NC_047559.1\t357799\t357801\n", "NC_047559.1\t357947\t357949\n", "\n", "==> zr3644_19_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-intron <==\n", "NC_047559.1\t62770\t62772\n", "NC_047559.1\t83475\t83477\n", "NC_047559.1\t100305\t100307\n", "NC_047559.1\t154324\t154326\n", "NC_047559.1\t154349\t154351\n", "NC_047559.1\t154507\t154509\n", "NC_047559.1\t164604\t164606\n", "NC_047559.1\t168950\t168952\n", "NC_047559.1\t255789\t255791\n", "NC_047559.1\t356303\t356305\n", "\n", "==> zr3644_19_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-intron <==\n", "NC_047559.1\t10155\t10157\n", "NC_047559.1\t10215\t10217\n", "NC_047559.1\t10270\t10272\n", "NC_047559.1\t10292\t10294\n", "NC_047559.1\t10314\t10316\n", "NC_047559.1\t10358\t10360\n", "NC_047559.1\t10402\t10404\n", "NC_047559.1\t10413\t10415\n", "NC_047559.1\t10457\t10459\n", "NC_047559.1\t10479\t10481\n", "\n", "==> zr3644_1_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-intron <==\n", "NC_047559.1\t68070\t68072\n", "NC_047559.1\t356378\t356380\n", "NC_047559.1\t356395\t356397\n", "NC_047559.1\t356910\t356912\n", "NC_047559.1\t356933\t356935\n", "NC_047559.1\t358586\t358588\n", "NC_047559.1\t359671\t359673\n", "NC_047559.1\t377838\t377840\n", "NC_047559.1\t420980\t420982\n", "NC_047559.1\t421032\t421034\n", "\n", "==> zr3644_1_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-intron <==\n", "NC_047559.1\t62935\t62937\n", "NC_047559.1\t68140\t68142\n", "NC_047559.1\t104216\t104218\n", "NC_047559.1\t117736\t117738\n", "NC_047559.1\t119924\t119926\n", "NC_047559.1\t159869\t159871\n", "NC_047559.1\t159881\t159883\n", "NC_047559.1\t160416\t160418\n", "NC_047559.1\t161179\t161181\n", "NC_047559.1\t162032\t162034\n", "\n", "==> zr3644_1_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-intron <==\n", "NC_047559.1\t10215\t10217\n", "NC_047559.1\t10270\t10272\n", "NC_047559.1\t10292\t10294\n", "NC_047559.1\t10314\t10316\n", "NC_047559.1\t10358\t10360\n", "NC_047559.1\t10380\t10382\n", "NC_047559.1\t10391\t10393\n", "NC_047559.1\t10402\t10404\n", "NC_047559.1\t10413\t10415\n", "NC_047559.1\t10457\t10459\n", "\n", "==> zr3644_20_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-intron <==\n", "NC_047559.1\t60313\t60315\n", "NC_047559.1\t60371\t60373\n", "NC_047559.1\t360361\t360363\n", "NC_047559.1\t416920\t416922\n", "NC_047559.1\t424894\t424896\n", "NC_047559.1\t424941\t424943\n", "NC_047559.1\t425000\t425002\n", "NC_047559.1\t425018\t425020\n", "NC_047559.1\t425106\t425108\n", "NC_047559.1\t425124\t425126\n", "\n", "==> zr3644_20_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-intron <==\n", "NC_047559.1\t62770\t62772\n", "NC_047559.1\t82012\t82014\n", "NC_047559.1\t82761\t82763\n", "NC_047559.1\t100249\t100251\n", "NC_047559.1\t100319\t100321\n", "NC_047559.1\t122867\t122869\n", "NC_047559.1\t153777\t153779\n", "NC_047559.1\t153830\t153832\n", "NC_047559.1\t153840\t153842\n", "NC_047559.1\t153850\t153852\n", "\n", "==> zr3644_20_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-intron <==\n", "NC_047559.1\t10270\t10272\n", "NC_047559.1\t10292\t10294\n", "NC_047559.1\t10314\t10316\n", "NC_047559.1\t10358\t10360\n", "NC_047559.1\t10402\t10404\n", "NC_047559.1\t10413\t10415\n", "NC_047559.1\t10479\t10481\n", "NC_047559.1\t10501\t10503\n", "NC_047559.1\t10545\t10547\n", "NC_047559.1\t10547\t10549\n", "\n", "==> zr3644_21_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-intron <==\n", "NC_047559.1\t356699\t356701\n", "NC_047559.1\t356910\t356912\n", "NC_047559.1\t356933\t356935\n", "NC_047559.1\t357501\t357503\n", "NC_047559.1\t357519\t357521\n", "NC_047559.1\t357751\t357753\n", "NC_047559.1\t357784\t357786\n", "NC_047559.1\t357799\t357801\n", "NC_047559.1\t419514\t419516\n", "NC_047559.1\t424694\t424696\n", "\n", "==> zr3644_21_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-intron <==\n", "NC_047559.1\t61081\t61083\n", "NC_047559.1\t104628\t104630\n", "NC_047559.1\t154324\t154326\n", "NC_047559.1\t154349\t154351\n", "NC_047559.1\t154507\t154509\n", "NC_047559.1\t227856\t227858\n", "NC_047559.1\t356335\t356337\n", "NC_047559.1\t356378\t356380\n", "NC_047559.1\t356395\t356397\n", "NC_047559.1\t356430\t356432\n", "\n", "==> zr3644_21_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-intron <==\n", "NC_047559.1\t10155\t10157\n", "NC_047559.1\t10215\t10217\n", "NC_047559.1\t10270\t10272\n", "NC_047559.1\t10292\t10294\n", "NC_047559.1\t10314\t10316\n", "NC_047559.1\t10479\t10481\n", "NC_047559.1\t10501\t10503\n", "NC_047559.1\t10545\t10547\n", "NC_047559.1\t10547\t10549\n", "NC_047559.1\t10645\t10647\n", "\n", "==> zr3644_22_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-intron <==\n", "NC_047559.1\t154324\t154326\n", "NC_047559.1\t356395\t356397\n", "NC_047559.1\t356430\t356432\n", "NC_047559.1\t356436\t356438\n", "NC_047559.1\t356532\t356534\n", "NC_047559.1\t358313\t358315\n", "NC_047559.1\t358375\t358377\n", "NC_047559.1\t358503\t358505\n", "NC_047559.1\t358527\t358529\n", "NC_047559.1\t360322\t360324\n", "\n", "==> zr3644_22_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-intron <==\n", "NC_047559.1\t62770\t62772\n", "NC_047559.1\t68070\t68072\n", "NC_047559.1\t100276\t100278\n", "NC_047559.1\t100319\t100321\n", "NC_047559.1\t154349\t154351\n", "NC_047559.1\t164915\t164917\n", "NC_047559.1\t166241\t166243\n", "NC_047559.1\t356335\t356337\n", "NC_047559.1\t356378\t356380\n", "NC_047559.1\t356685\t356687\n", "\n", "==> zr3644_22_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-intron <==\n", "NC_047559.1\t10155\t10157\n", "NC_047559.1\t10270\t10272\n", "NC_047559.1\t10292\t10294\n", "NC_047559.1\t10314\t10316\n", "NC_047559.1\t10457\t10459\n", "NC_047559.1\t10479\t10481\n", "NC_047559.1\t10501\t10503\n", "NC_047559.1\t10545\t10547\n", "NC_047559.1\t10547\t10549\n", "NC_047559.1\t10567\t10569\n", "\n", "==> zr3644_23_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-intron <==\n", "NC_047559.1\t356335\t356337\n", "NC_047559.1\t356378\t356380\n", "NC_047559.1\t356395\t356397\n", "NC_047559.1\t356430\t356432\n", "NC_047559.1\t356436\t356438\n", "NC_047559.1\t356832\t356834\n", "NC_047559.1\t356933\t356935\n", "NC_047559.1\t357784\t357786\n", "NC_047559.1\t357799\t357801\n", "NC_047559.1\t358313\t358315\n", "\n", "==> zr3644_23_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-intron <==\n", "NC_047559.1\t62770\t62772\n", "NC_047559.1\t104267\t104269\n", "NC_047559.1\t123167\t123169\n", "NC_047559.1\t154349\t154351\n", "NC_047559.1\t154507\t154509\n", "NC_047559.1\t160757\t160759\n", "NC_047559.1\t160765\t160767\n", "NC_047559.1\t160827\t160829\n", "NC_047559.1\t160832\t160834\n", "NC_047559.1\t160838\t160840\n", "\n", "==> zr3644_23_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-intron <==\n", "NC_047559.1\t10270\t10272\n", "NC_047559.1\t10292\t10294\n", "NC_047559.1\t10314\t10316\n", "NC_047559.1\t10358\t10360\n", "NC_047559.1\t10545\t10547\n", "NC_047559.1\t10547\t10549\n", "NC_047559.1\t10567\t10569\n", "NC_047559.1\t10592\t10594\n", "NC_047559.1\t10772\t10774\n", "NC_047559.1\t10845\t10847\n", "\n", "==> zr3644_24_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-intron <==\n", "NC_047559.1\t356436\t356438\n", "NC_047559.1\t356910\t356912\n", "NC_047559.1\t356933\t356935\n", "NC_047559.1\t357751\t357753\n", "NC_047559.1\t357784\t357786\n", "NC_047559.1\t357799\t357801\n", "NC_047559.1\t357900\t357902\n", "NC_047559.1\t357947\t357949\n", "NC_047559.1\t357955\t357957\n", "NC_047559.1\t358035\t358037\n", "\n", "==> zr3644_24_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-intron <==\n", "NC_047559.1\t10547\t10549\n", "NC_047559.1\t10645\t10647\n", "NC_047559.1\t62770\t62772\n", "NC_047559.1\t100751\t100753\n", "NC_047559.1\t113151\t113153\n", "NC_047559.1\t120270\t120272\n", "NC_047559.1\t122957\t122959\n", "NC_047559.1\t153815\t153817\n", "NC_047559.1\t153830\t153832\n", "NC_047559.1\t153840\t153842\n", "\n", "==> zr3644_24_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-intron <==\n", "NC_047559.1\t10270\t10272\n", "NC_047559.1\t10292\t10294\n", "NC_047559.1\t10314\t10316\n", "NC_047559.1\t10545\t10547\n", "NC_047559.1\t10567\t10569\n", "NC_047559.1\t10592\t10594\n", "NC_047559.1\t10612\t10614\n", "NC_047559.1\t10667\t10669\n", "NC_047559.1\t10772\t10774\n", "NC_047559.1\t10845\t10847\n", "\n", "==> zr3644_2_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-intron <==\n", "NC_047559.1\t61081\t61083\n", "NC_047559.1\t359678\t359680\n", "NC_047559.1\t360322\t360324\n", "NC_047559.1\t360361\t360363\n", "NC_047559.1\t424894\t424896\n", "NC_047559.1\t424941\t424943\n", "NC_047559.1\t425000\t425002\n", "NC_047559.1\t425018\t425020\n", "NC_047559.1\t425065\t425067\n", "NC_047559.1\t425106\t425108\n", "\n", "==> zr3644_2_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-intron <==\n", "NC_047559.1\t10501\t10503\n", "NC_047559.1\t10772\t10774\n", "NC_047559.1\t10845\t10847\n", "NC_047559.1\t62770\t62772\n", "NC_047559.1\t68070\t68072\n", "NC_047559.1\t100180\t100182\n", "NC_047559.1\t104439\t104441\n", "NC_047559.1\t104697\t104699\n", "NC_047559.1\t113151\t113153\n", "NC_047559.1\t123805\t123807\n", "\n", "==> zr3644_2_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-intron <==\n", "NC_047559.1\t10155\t10157\n", "NC_047559.1\t10270\t10272\n", "NC_047559.1\t10292\t10294\n", "NC_047559.1\t10314\t10316\n", "NC_047559.1\t10358\t10360\n", "NC_047559.1\t10380\t10382\n", "NC_047559.1\t10391\t10393\n", "NC_047559.1\t10402\t10404\n", "NC_047559.1\t10413\t10415\n", "NC_047559.1\t10457\t10459\n", "\n", "==> zr3644_3_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-intron <==\n", "NC_047559.1\t356933\t356935\n", "NC_047559.1\t357519\t357521\n", "NC_047559.1\t357751\t357753\n", "NC_047559.1\t357784\t357786\n", "NC_047559.1\t357799\t357801\n", "NC_047559.1\t424894\t424896\n", "NC_047559.1\t424941\t424943\n", "NC_047559.1\t425000\t425002\n", "NC_047559.1\t425018\t425020\n", "NC_047559.1\t425106\t425108\n", "\n", "==> zr3644_3_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-intron <==\n", "NC_047559.1\t62770\t62772\n", "NC_047559.1\t100276\t100278\n", "NC_047559.1\t115724\t115726\n", "NC_047559.1\t154507\t154509\n", "NC_047559.1\t169652\t169654\n", "NC_047559.1\t227983\t227985\n", "NC_047559.1\t356303\t356305\n", "NC_047559.1\t356335\t356337\n", "NC_047559.1\t356378\t356380\n", "NC_047559.1\t356395\t356397\n", "\n", "==> zr3644_3_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-intron <==\n", "NC_047559.1\t10215\t10217\n", "NC_047559.1\t10270\t10272\n", "NC_047559.1\t10292\t10294\n", "NC_047559.1\t10314\t10316\n", "NC_047559.1\t10358\t10360\n", "NC_047559.1\t10402\t10404\n", "NC_047559.1\t10413\t10415\n", "NC_047559.1\t10457\t10459\n", "NC_047559.1\t10479\t10481\n", "NC_047559.1\t10501\t10503\n", "\n", "==> zr3644_4_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-intron <==\n", "NC_047559.1\t154507\t154509\n", "NC_047559.1\t356395\t356397\n", "NC_047559.1\t356436\t356438\n", "NC_047559.1\t356699\t356701\n", "NC_047559.1\t356748\t356750\n", "NC_047559.1\t356910\t356912\n", "NC_047559.1\t356933\t356935\n", "NC_047559.1\t357362\t357364\n", "NC_047559.1\t357382\t357384\n", "NC_047559.1\t357396\t357398\n", "\n", "==> zr3644_4_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-intron <==\n", "NC_047559.1\t10479\t10481\n", "NC_047559.1\t61081\t61083\n", "NC_047559.1\t61203\t61205\n", "NC_047559.1\t62770\t62772\n", "NC_047559.1\t109247\t109249\n", "NC_047559.1\t113151\t113153\n", "NC_047559.1\t153840\t153842\n", "NC_047559.1\t154349\t154351\n", "NC_047559.1\t160124\t160126\n", "NC_047559.1\t160131\t160133\n", "\n", "==> zr3644_4_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-intron <==\n", "NC_047559.1\t10155\t10157\n", "NC_047559.1\t10270\t10272\n", "NC_047559.1\t10292\t10294\n", "NC_047559.1\t10314\t10316\n", "NC_047559.1\t10358\t10360\n", "NC_047559.1\t10501\t10503\n", "NC_047559.1\t10545\t10547\n", "NC_047559.1\t10547\t10549\n", "NC_047559.1\t10567\t10569\n", "NC_047559.1\t10592\t10594\n", "\n", "==> zr3644_5_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-intron <==\n", "NC_047559.1\t356335\t356337\n", "NC_047559.1\t356378\t356380\n", "NC_047559.1\t356395\t356397\n", "NC_047559.1\t356430\t356432\n", "NC_047559.1\t356436\t356438\n", "NC_047559.1\t357362\t357364\n", "NC_047559.1\t357382\t357384\n", "NC_047559.1\t357396\t357398\n", "NC_047559.1\t357405\t357407\n", "NC_047559.1\t357501\t357503\n", "\n", "==> zr3644_5_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-intron <==\n", "NC_047559.1\t61081\t61083\n", "NC_047559.1\t62770\t62772\n", "NC_047559.1\t153880\t153882\n", "NC_047559.1\t159881\t159883\n", "NC_047559.1\t168725\t168727\n", "NC_047559.1\t184076\t184078\n", "NC_047559.1\t356532\t356534\n", "NC_047559.1\t356910\t356912\n", "NC_047559.1\t356933\t356935\n", "NC_047559.1\t357519\t357521\n", "\n", "==> zr3644_5_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-intron <==\n", "NC_047559.1\t10155\t10157\n", "NC_047559.1\t10215\t10217\n", "NC_047559.1\t10270\t10272\n", "NC_047559.1\t10292\t10294\n", "NC_047559.1\t10314\t10316\n", "NC_047559.1\t10358\t10360\n", "NC_047559.1\t10402\t10404\n", "NC_047559.1\t10413\t10415\n", "NC_047559.1\t10457\t10459\n", "NC_047559.1\t10479\t10481\n", "\n", "==> zr3644_6_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-intron <==\n", "NC_047559.1\t356685\t356687\n", "NC_047559.1\t357501\t357503\n", "NC_047559.1\t357519\t357521\n", "NC_047559.1\t357799\t357801\n", "NC_047559.1\t360361\t360363\n", "NC_047559.1\t419606\t419608\n", "NC_047559.1\t419784\t419786\n", "NC_047559.1\t422513\t422515\n", "NC_047559.1\t424941\t424943\n", "NC_047559.1\t425000\t425002\n", "\n", "==> zr3644_6_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-intron <==\n", "NC_047559.1\t61081\t61083\n", "NC_047559.1\t62770\t62772\n", "NC_047559.1\t68070\t68072\n", "NC_047559.1\t100154\t100156\n", "NC_047559.1\t113151\t113153\n", "NC_047559.1\t113369\t113371\n", "NC_047559.1\t154324\t154326\n", "NC_047559.1\t154349\t154351\n", "NC_047559.1\t154507\t154509\n", "NC_047559.1\t157684\t157686\n", "\n", "==> zr3644_6_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-intron <==\n", "NC_047559.1\t10155\t10157\n", "NC_047559.1\t10215\t10217\n", "NC_047559.1\t10270\t10272\n", "NC_047559.1\t10292\t10294\n", "NC_047559.1\t10314\t10316\n", "NC_047559.1\t10457\t10459\n", "NC_047559.1\t10479\t10481\n", "NC_047559.1\t10501\t10503\n", "NC_047559.1\t10545\t10547\n", "NC_047559.1\t10547\t10549\n", "\n", "==> zr3644_7_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-intron <==\n", "NC_047559.1\t356378\t356380\n", "NC_047559.1\t356395\t356397\n", "NC_047559.1\t356430\t356432\n", "NC_047559.1\t356436\t356438\n", "NC_047559.1\t356532\t356534\n", "NC_047559.1\t356748\t356750\n", "NC_047559.1\t356910\t356912\n", "NC_047559.1\t356933\t356935\n", "NC_047559.1\t357784\t357786\n", "NC_047559.1\t357955\t357957\n", "\n", "==> zr3644_7_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-intron <==\n", "NC_047559.1\t10380\t10382\n", "NC_047559.1\t61203\t61205\n", "NC_047559.1\t62770\t62772\n", "NC_047559.1\t62935\t62937\n", "NC_047559.1\t71969\t71971\n", "NC_047559.1\t71973\t71975\n", "NC_047559.1\t71994\t71996\n", "NC_047559.1\t71998\t72000\n", "NC_047559.1\t72014\t72016\n", "NC_047559.1\t72018\t72020\n", "\n", "==> zr3644_7_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-intron <==\n", "NC_047559.1\t10155\t10157\n", "NC_047559.1\t10215\t10217\n", "NC_047559.1\t10270\t10272\n", "NC_047559.1\t10292\t10294\n", "NC_047559.1\t10314\t10316\n", "NC_047559.1\t10358\t10360\n", "NC_047559.1\t10391\t10393\n", "NC_047559.1\t10402\t10404\n", "NC_047559.1\t10413\t10415\n", "NC_047559.1\t10457\t10459\n", "\n", "==> zr3644_8_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-intron <==\n", "NC_047559.1\t378417\t378419\n", "NC_047559.1\t378455\t378457\n", "NC_047559.1\t424894\t424896\n", "NC_047559.1\t424941\t424943\n", "NC_047559.1\t425000\t425002\n", "NC_047559.1\t425018\t425020\n", "NC_047559.1\t425106\t425108\n", "NC_047559.1\t425124\t425126\n", "NC_047559.1\t425144\t425146\n", "NC_047559.1\t425159\t425161\n", "\n", "==> zr3644_8_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-intron <==\n", "NC_047559.1\t84487\t84489\n", "NC_047559.1\t154324\t154326\n", "NC_047559.1\t154349\t154351\n", "NC_047559.1\t154507\t154509\n", "NC_047559.1\t157657\t157659\n", "NC_047559.1\t157684\t157686\n", "NC_047559.1\t157687\t157689\n", "NC_047559.1\t157725\t157727\n", "NC_047559.1\t160736\t160738\n", "NC_047559.1\t362766\t362768\n", "\n", "==> zr3644_8_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-intron <==\n", "NC_047559.1\t10270\t10272\n", "NC_047559.1\t10292\t10294\n", "NC_047559.1\t10314\t10316\n", "NC_047559.1\t10413\t10415\n", "NC_047559.1\t10457\t10459\n", "NC_047559.1\t10479\t10481\n", "NC_047559.1\t10501\t10503\n", "NC_047559.1\t10545\t10547\n", "NC_047559.1\t10547\t10549\n", "NC_047559.1\t10567\t10569\n", "\n", "==> zr3644_9_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-intron <==\n", "NC_047559.1\t359664\t359666\n", "NC_047559.1\t359671\t359673\n", "NC_047559.1\t359678\t359680\n", "NC_047559.1\t417944\t417946\n", "NC_047559.1\t419514\t419516\n", "NC_047559.1\t419784\t419786\n", "NC_047559.1\t420583\t420585\n", "NC_047559.1\t420980\t420982\n", "NC_047559.1\t424941\t424943\n", "NC_047559.1\t425000\t425002\n", "\n", "==> zr3644_9_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-intron <==\n", "NC_047559.1\t62770\t62772\n", "NC_047559.1\t68140\t68142\n", "NC_047559.1\t100154\t100156\n", "NC_047559.1\t100180\t100182\n", "NC_047559.1\t100249\t100251\n", "NC_047559.1\t100305\t100307\n", "NC_047559.1\t104313\t104315\n", "NC_047559.1\t104324\t104326\n", "NC_047559.1\t114971\t114973\n", "NC_047559.1\t115632\t115634\n", "\n", "==> zr3644_9_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-intron <==\n", "NC_047559.1\t10391\t10393\n", "NC_047559.1\t10402\t10404\n", "NC_047559.1\t10413\t10415\n", "NC_047559.1\t10845\t10847\n", "NC_047559.1\t10859\t10861\n", "NC_047559.1\t14770\t14772\n", "NC_047559.1\t14790\t14792\n", "NC_047559.1\t15481\t15483\n", "NC_047559.1\t15489\t15491\n", "NC_047559.1\t15538\t15540\n", "\n", "==> zr3644_union-averages_5x.bedgraph-Meth.bed-intron <==\n", "NC_047559.1\t60313\t60315\n", "NC_047559.1\t60371\t60373\n", "NC_047559.1\t358586\t358588\n", "NC_047559.1\t359664\t359666\n", "NC_047559.1\t359671\t359673\n", "NC_047559.1\t360322\t360324\n", "NC_047559.1\t360361\t360363\n", "NC_047559.1\t383390\t383392\n", "NC_047559.1\t383394\t383396\n", "NC_047559.1\t417944\t417946\n", "\n", "==> zr3644_union-averages_5x.bedgraph-sparseMeth.bed-intron <==\n", "NC_047559.1\t60430\t60432\n", "NC_047559.1\t61081\t61083\n", "NC_047559.1\t62770\t62772\n", "NC_047559.1\t62935\t62937\n", "NC_047559.1\t68070\t68072\n", "NC_047559.1\t68140\t68142\n", "NC_047559.1\t72245\t72247\n", "NC_047559.1\t84068\t84070\n", "NC_047559.1\t100964\t100966\n", "NC_047559.1\t107909\t107911\n", "\n", "==> zr3644_union-averages_5x.bedgraph-unMeth.bed-intron <==\n", "NC_047559.1\t10155\t10157\n", "NC_047559.1\t10215\t10217\n", "NC_047559.1\t10270\t10272\n", "NC_047559.1\t10292\t10294\n", "NC_047559.1\t10314\t10316\n", "NC_047559.1\t10358\t10360\n", "NC_047559.1\t10380\t10382\n", "NC_047559.1\t10391\t10393\n", "NC_047559.1\t10402\t10404\n", "NC_047559.1\t10413\t10415\n" ] } ], "source": [ "#Check output\n", "!head *intron" ] }, { "cell_type": "code", "execution_count": 53, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ " 361376 zr3644_10_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-intron\n", " 282419 zr3644_10_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-intron\n", " 1858030 zr3644_10_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-intron\n", " 369981 zr3644_11_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-intron\n", " 297780 zr3644_11_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-intron\n", " 1959575 zr3644_11_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-intron\n", " 324571 zr3644_12_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-intron\n", " 268438 zr3644_12_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-intron\n", " 1798371 zr3644_12_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-intron\n", " 362006 zr3644_13_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-intron\n", " 306884 zr3644_13_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-intron\n", " 1915185 zr3644_13_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-intron\n", " 345011 zr3644_14_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-intron\n", " 179871 zr3644_14_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-intron\n", " 1443052 zr3644_14_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-intron\n", " 421206 zr3644_15_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-intron\n", " 312321 zr3644_15_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-intron\n", " 1964910 zr3644_15_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-intron\n", " 332791 zr3644_16_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-intron\n", " 266862 zr3644_16_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-intron\n", " 1755730 zr3644_16_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-intron\n", " 352455 zr3644_17_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-intron\n", " 258532 zr3644_17_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-intron\n", " 1918248 zr3644_17_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-intron\n", " 339902 zr3644_18_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-intron\n", " 281986 zr3644_18_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-intron\n", " 1817005 zr3644_18_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-intron\n", " 327662 zr3644_19_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-intron\n", " 271027 zr3644_19_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-intron\n", " 1809928 zr3644_19_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-intron\n", " 287196 zr3644_1_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-intron\n", " 277903 zr3644_1_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-intron\n", " 1791869 zr3644_1_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-intron\n", " 351686 zr3644_20_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-intron\n", " 296114 zr3644_20_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-intron\n", " 1895166 zr3644_20_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-intron\n", " 350616 zr3644_21_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-intron\n", " 295820 zr3644_21_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-intron\n", " 1863825 zr3644_21_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-intron\n", " 318929 zr3644_22_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-intron\n", " 264175 zr3644_22_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-intron\n", " 1746103 zr3644_22_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-intron\n", " 281603 zr3644_23_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-intron\n", " 236199 zr3644_23_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-intron\n", " 1549277 zr3644_23_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-intron\n", " 344989 zr3644_24_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-intron\n", " 282734 zr3644_24_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-intron\n", " 1857424 zr3644_24_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-intron\n", " 360323 zr3644_2_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-intron\n", " 259040 zr3644_2_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-intron\n", " 1960844 zr3644_2_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-intron\n", " 289806 zr3644_3_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-intron\n", " 240745 zr3644_3_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-intron\n", " 1570378 zr3644_3_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-intron\n", " 333542 zr3644_4_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-intron\n", " 275143 zr3644_4_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-intron\n", " 1836562 zr3644_4_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-intron\n", " 317155 zr3644_5_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-intron\n", " 266854 zr3644_5_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-intron\n", " 1706973 zr3644_5_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-intron\n", " 351361 zr3644_6_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-intron\n", " 288975 zr3644_6_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-intron\n", " 1892236 zr3644_6_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-intron\n", " 436868 zr3644_7_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-intron\n", " 358324 zr3644_7_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-intron\n", " 2346183 zr3644_7_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-intron\n", " 309795 zr3644_8_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-intron\n", " 249808 zr3644_8_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-intron\n", " 1643455 zr3644_8_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-intron\n", " 320933 zr3644_9_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-intron\n", " 265625 zr3644_9_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-intron\n", " 1667596 zr3644_9_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-intron\n", " 526656 zr3644_union-averages_5x.bedgraph-Meth.bed-intron\n", " 491559 zr3644_union-averages_5x.bedgraph-sparseMeth.bed-intron\n", " 3135220 zr3644_union-averages_5x.bedgraph-unMeth.bed-intron\n", " 62496702 total\n" ] } ], "source": [ "#Count number of overlaps\n", "!wc -l *intron" ] }, { "cell_type": "code", "execution_count": 54, "metadata": { "collapsed": true }, "outputs": [], "source": [ "#Get line counts for each fine\n", "# Remove 76th line (total entries)\n", "#Ensure output is tab-delimited\n", "#Save output\n", "!wc -l *-intron \\\n", "| sed '76,$ d' \\\n", "| awk '{print $1\"\\t\"$2}' \\\n", "> zr3644_5x-intron-counts.txt" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "### 6f. Upstream flanks" ] }, { "cell_type": "code", "execution_count": 75, "metadata": { "collapsed": false }, "outputs": [], "source": [ "%%bash\n", "for f in *bed\n", "do\n", " /Users/Shared/bioinformatics/bedtools2/bin/intersectBed \\\n", " -u \\\n", " -a ${f} \\\n", " -b /Volumes/web-1/halfshell/genomic-databank/cgigas_uk_roslin_v1_upstream.gff \\\n", " > ${f}-upstreamFlanks\n", "done" ] }, { "cell_type": "code", "execution_count": 76, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "==> zr3644_10_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-upstreamFlanks <==\n", "NC_047559.1\t576634\t576636\n", "NC_047559.1\t576693\t576695\n", "NC_047559.1\t576752\t576754\n", "NC_047559.1\t1800772\t1800774\n", "NC_047559.1\t1801087\t1801089\n", "NC_047559.1\t1801099\t1801101\n", "NC_047559.1\t1801111\t1801113\n", "NC_047559.1\t1801125\t1801127\n", "NC_047559.1\t3158461\t3158463\n", "NC_047559.1\t3907322\t3907324\n", "\n", "==> zr3644_10_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-upstreamFlanks <==\n", "NC_047559.1\t8979\t8981\n", "NC_047559.1\t9122\t9124\n", "NC_047559.1\t9140\t9142\n", "NC_047559.1\t142484\t142486\n", "NC_047559.1\t335878\t335880\n", "NC_047559.1\t335886\t335888\n", "NC_047559.1\t335892\t335894\n", "NC_047559.1\t335912\t335914\n", "NC_047559.1\t335932\t335934\n", "NC_047559.1\t778316\t778318\n", "\n", "==> zr3644_10_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-upstreamFlanks <==\n", "NC_047559.1\t8970\t8972\n", "NC_047559.1\t9159\t9161\n", "NC_047559.1\t9237\t9239\n", "NC_047559.1\t9240\t9242\n", "NC_047559.1\t9774\t9776\n", "NC_047559.1\t9781\t9783\n", "NC_047559.1\t9787\t9789\n", "NC_047559.1\t9795\t9797\n", "NC_047559.1\t9803\t9805\n", "NC_047559.1\t9817\t9819\n", "\n", "==> zr3644_11_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-upstreamFlanks <==\n", "NC_047559.1\t141777\t141779\n", "NC_047559.1\t142406\t142408\n", "NC_047559.1\t142411\t142413\n", "NC_047559.1\t142424\t142426\n", "NC_047559.1\t142447\t142449\n", "NC_047559.1\t142451\t142453\n", "NC_047559.1\t142465\t142467\n", "NC_047559.1\t142484\t142486\n", "NC_047559.1\t576308\t576310\n", "NC_047559.1\t576634\t576636\n", "\n", "==> zr3644_11_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-upstreamFlanks <==\n", "NC_047559.1\t9122\t9124\n", "NC_047559.1\t9140\t9142\n", "NC_047559.1\t9159\t9161\n", "NC_047559.1\t142504\t142506\n", "NC_047559.1\t243319\t243321\n", "NC_047559.1\t472474\t472476\n", "NC_047559.1\t702986\t702988\n", "NC_047559.1\t703403\t703405\n", "NC_047559.1\t703439\t703441\n", "NC_047559.1\t1050622\t1050624\n", "\n", "==> zr3644_11_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-upstreamFlanks <==\n", "NC_047559.1\t8970\t8972\n", "NC_047559.1\t8979\t8981\n", "NC_047559.1\t9237\t9239\n", "NC_047559.1\t9240\t9242\n", "NC_047559.1\t9658\t9660\n", "NC_047559.1\t9661\t9663\n", "NC_047559.1\t9664\t9666\n", "NC_047559.1\t9774\t9776\n", "NC_047559.1\t9781\t9783\n", "NC_047559.1\t9787\t9789\n", "\n", "==> zr3644_12_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-upstreamFlanks <==\n", "NC_047559.1\t9122\t9124\n", "NC_047559.1\t141751\t141753\n", "NC_047559.1\t141777\t141779\n", "NC_047559.1\t576308\t576310\n", "NC_047559.1\t576634\t576636\n", "NC_047559.1\t576693\t576695\n", "NC_047559.1\t576752\t576754\n", "NC_047559.1\t3158461\t3158463\n", "NC_047559.1\t3158489\t3158491\n", "NC_047559.1\t3907322\t3907324\n", "\n", "==> zr3644_12_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-upstreamFlanks <==\n", "NC_047559.1\t9237\t9239\n", "NC_047559.1\t9240\t9242\n", "NC_047559.1\t225940\t225942\n", "NC_047559.1\t243804\t243806\n", "NC_047559.1\t335960\t335962\n", "NC_047559.1\t336002\t336004\n", "NC_047559.1\t336093\t336095\n", "NC_047559.1\t336111\t336113\n", "NC_047559.1\t452744\t452746\n", "NC_047559.1\t631946\t631948\n", "\n", "==> zr3644_12_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-upstreamFlanks <==\n", "NC_047559.1\t9140\t9142\n", "NC_047559.1\t9159\t9161\n", "NC_047559.1\t9658\t9660\n", "NC_047559.1\t9661\t9663\n", "NC_047559.1\t9664\t9666\n", "NC_047559.1\t9774\t9776\n", "NC_047559.1\t9781\t9783\n", "NC_047559.1\t9787\t9789\n", "NC_047559.1\t9795\t9797\n", "NC_047559.1\t9803\t9805\n", "\n", "==> zr3644_13_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-upstreamFlanks <==\n", "NC_047559.1\t576308\t576310\n", "NC_047559.1\t576634\t576636\n", "NC_047559.1\t576693\t576695\n", "NC_047559.1\t576752\t576754\n", "NC_047559.1\t3158489\t3158491\n", "NC_047559.1\t3837935\t3837937\n", "NC_047559.1\t3837940\t3837942\n", "NC_047559.1\t3907203\t3907205\n", "NC_047559.1\t3907322\t3907324\n", "NC_047559.1\t3907684\t3907686\n", "\n", "==> zr3644_13_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-upstreamFlanks <==\n", "NC_047559.1\t9122\t9124\n", "NC_047559.1\t9140\t9142\n", "NC_047559.1\t9159\t9161\n", "NC_047559.1\t9237\t9239\n", "NC_047559.1\t9240\t9242\n", "NC_047559.1\t13634\t13636\n", "NC_047559.1\t142484\t142486\n", "NC_047559.1\t142490\t142492\n", "NC_047559.1\t268073\t268075\n", "NC_047559.1\t268575\t268577\n", "\n", "==> zr3644_13_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-upstreamFlanks <==\n", "NC_047559.1\t8970\t8972\n", "NC_047559.1\t8979\t8981\n", "NC_047559.1\t9658\t9660\n", "NC_047559.1\t9661\t9663\n", "NC_047559.1\t9664\t9666\n", "NC_047559.1\t9774\t9776\n", "NC_047559.1\t9781\t9783\n", "NC_047559.1\t9787\t9789\n", "NC_047559.1\t9795\t9797\n", "NC_047559.1\t9803\t9805\n", "\n", "==> zr3644_14_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-upstreamFlanks <==\n", "NC_047559.1\t576308\t576310\n", "NC_047559.1\t576634\t576636\n", "NC_047559.1\t576693\t576695\n", "NC_047559.1\t576752\t576754\n", "NC_047559.1\t3158461\t3158463\n", "NC_047559.1\t3819401\t3819403\n", "NC_047559.1\t3819453\t3819455\n", "NC_047559.1\t3819488\t3819490\n", "NC_047559.1\t3819925\t3819927\n", "NC_047559.1\t3819934\t3819936\n", "\n", "==> zr3644_14_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-upstreamFlanks <==\n", "NC_047559.1\t9603\t9605\n", "NC_047559.1\t141751\t141753\n", "NC_047559.1\t254230\t254232\n", "NC_047559.1\t354919\t354921\n", "NC_047559.1\t702986\t702988\n", "NC_047559.1\t768116\t768118\n", "NC_047559.1\t784626\t784628\n", "NC_047559.1\t1101223\t1101225\n", "NC_047559.1\t1131021\t1131023\n", "NC_047559.1\t1266270\t1266272\n", "\n", "==> zr3644_14_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-upstreamFlanks <==\n", "NC_047559.1\t9658\t9660\n", "NC_047559.1\t9661\t9663\n", "NC_047559.1\t9664\t9666\n", "NC_047559.1\t9774\t9776\n", "NC_047559.1\t9781\t9783\n", "NC_047559.1\t9787\t9789\n", "NC_047559.1\t9795\t9797\n", "NC_047559.1\t9803\t9805\n", "NC_047559.1\t9817\t9819\n", "NC_047559.1\t13280\t13282\n", "\n", "==> zr3644_15_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-upstreamFlanks <==\n", "NC_047559.1\t141708\t141710\n", "NC_047559.1\t141751\t141753\n", "NC_047559.1\t141777\t141779\n", "NC_047559.1\t141853\t141855\n", "NC_047559.1\t141858\t141860\n", "NC_047559.1\t141894\t141896\n", "NC_047559.1\t142406\t142408\n", "NC_047559.1\t142411\t142413\n", "NC_047559.1\t142424\t142426\n", "NC_047559.1\t576308\t576310\n", "\n", "==> zr3644_15_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-upstreamFlanks <==\n", "NC_047559.1\t8979\t8981\n", "NC_047559.1\t9122\t9124\n", "NC_047559.1\t9140\t9142\n", "NC_047559.1\t9159\t9161\n", "NC_047559.1\t9774\t9776\n", "NC_047559.1\t9781\t9783\n", "NC_047559.1\t9787\t9789\n", "NC_047559.1\t9795\t9797\n", "NC_047559.1\t9803\t9805\n", "NC_047559.1\t9817\t9819\n", "\n", "==> zr3644_15_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-upstreamFlanks <==\n", "NC_047559.1\t8970\t8972\n", "NC_047559.1\t9237\t9239\n", "NC_047559.1\t9240\t9242\n", "NC_047559.1\t9658\t9660\n", "NC_047559.1\t9661\t9663\n", "NC_047559.1\t9664\t9666\n", "NC_047559.1\t13156\t13158\n", "NC_047559.1\t13182\t13184\n", "NC_047559.1\t13186\t13188\n", "NC_047559.1\t13194\t13196\n", "\n", "==> zr3644_16_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-upstreamFlanks <==\n", "NC_047559.1\t335850\t335852\n", "NC_047559.1\t335858\t335860\n", "NC_047559.1\t576634\t576636\n", "NC_047559.1\t576693\t576695\n", "NC_047559.1\t576752\t576754\n", "NC_047559.1\t2190175\t2190177\n", "NC_047559.1\t2190292\t2190294\n", "NC_047559.1\t2190303\t2190305\n", "NC_047559.1\t3158461\t3158463\n", "NC_047559.1\t3158489\t3158491\n", "\n", "==> zr3644_16_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-upstreamFlanks <==\n", "NC_047559.1\t8970\t8972\n", "NC_047559.1\t8979\t8981\n", "NC_047559.1\t9122\t9124\n", "NC_047559.1\t9140\t9142\n", "NC_047559.1\t9159\t9161\n", "NC_047559.1\t226270\t226272\n", "NC_047559.1\t328514\t328516\n", "NC_047559.1\t328531\t328533\n", "NC_047559.1\t328575\t328577\n", "NC_047559.1\t328607\t328609\n", "\n", "==> zr3644_16_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-upstreamFlanks <==\n", "NC_047559.1\t9237\t9239\n", "NC_047559.1\t9240\t9242\n", "NC_047559.1\t9774\t9776\n", "NC_047559.1\t9781\t9783\n", "NC_047559.1\t9787\t9789\n", "NC_047559.1\t9795\t9797\n", "NC_047559.1\t9803\t9805\n", "NC_047559.1\t9817\t9819\n", "NC_047559.1\t13156\t13158\n", "NC_047559.1\t13182\t13184\n", "\n", "==> zr3644_17_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-upstreamFlanks <==\n", "NC_047559.1\t576308\t576310\n", "NC_047559.1\t576634\t576636\n", "NC_047559.1\t576693\t576695\n", "NC_047559.1\t576752\t576754\n", "NC_047559.1\t2190095\t2190097\n", "NC_047559.1\t2190175\t2190177\n", "NC_047559.1\t2190215\t2190217\n", "NC_047559.1\t2190292\t2190294\n", "NC_047559.1\t2190303\t2190305\n", "NC_047559.1\t2190335\t2190337\n", "\n", "==> zr3644_17_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-upstreamFlanks <==\n", "NC_047559.1\t79573\t79575\n", "NC_047559.1\t79581\t79583\n", "NC_047559.1\t79757\t79759\n", "NC_047559.1\t142465\t142467\n", "NC_047559.1\t142484\t142486\n", "NC_047559.1\t142490\t142492\n", "NC_047559.1\t142504\t142506\n", "NC_047559.1\t268592\t268594\n", "NC_047559.1\t452807\t452809\n", "NC_047559.1\t637967\t637969\n", "\n", "==> zr3644_17_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-upstreamFlanks <==\n", "NC_047559.1\t9122\t9124\n", "NC_047559.1\t9140\t9142\n", "NC_047559.1\t9159\t9161\n", "NC_047559.1\t9237\t9239\n", "NC_047559.1\t9240\t9242\n", "NC_047559.1\t9774\t9776\n", "NC_047559.1\t9781\t9783\n", "NC_047559.1\t9787\t9789\n", "NC_047559.1\t9795\t9797\n", "NC_047559.1\t9803\t9805\n", "\n", "==> zr3644_18_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-upstreamFlanks <==\n", "NC_047559.1\t142424\t142426\n", "NC_047559.1\t142447\t142449\n", "NC_047559.1\t142451\t142453\n", "NC_047559.1\t142465\t142467\n", "NC_047559.1\t576634\t576636\n", "NC_047559.1\t576693\t576695\n", "NC_047559.1\t576752\t576754\n", "NC_047559.1\t3158542\t3158544\n", "NC_047559.1\t3158566\t3158568\n", "NC_047559.1\t3907322\t3907324\n", "\n", "==> zr3644_18_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-upstreamFlanks <==\n", "NC_047559.1\t9122\t9124\n", "NC_047559.1\t9140\t9142\n", "NC_047559.1\t9787\t9789\n", "NC_047559.1\t13595\t13597\n", "NC_047559.1\t141708\t141710\n", "NC_047559.1\t141717\t141719\n", "NC_047559.1\t141751\t141753\n", "NC_047559.1\t141777\t141779\n", "NC_047559.1\t141800\t141802\n", "NC_047559.1\t141853\t141855\n", "\n", "==> zr3644_18_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-upstreamFlanks <==\n", "NC_047559.1\t8970\t8972\n", "NC_047559.1\t8979\t8981\n", "NC_047559.1\t9159\t9161\n", "NC_047559.1\t9237\t9239\n", "NC_047559.1\t9240\t9242\n", "NC_047559.1\t9658\t9660\n", "NC_047559.1\t9661\t9663\n", "NC_047559.1\t9664\t9666\n", "NC_047559.1\t9774\t9776\n", "NC_047559.1\t9781\t9783\n", "\n", "==> zr3644_19_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-upstreamFlanks <==\n", "NC_047559.1\t141800\t141802\n", "NC_047559.1\t141853\t141855\n", "NC_047559.1\t141858\t141860\n", "NC_047559.1\t576634\t576636\n", "NC_047559.1\t576693\t576695\n", "NC_047559.1\t576752\t576754\n", "NC_047559.1\t3907322\t3907324\n", "NC_047559.1\t3907587\t3907589\n", "NC_047559.1\t4539424\t4539426\n", "NC_047559.1\t4539447\t4539449\n", "\n", "==> zr3644_19_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-upstreamFlanks <==\n", "NC_047559.1\t9122\t9124\n", "NC_047559.1\t9140\t9142\n", "NC_047559.1\t9237\t9239\n", "NC_047559.1\t9240\t9242\n", "NC_047559.1\t141708\t141710\n", "NC_047559.1\t141717\t141719\n", "NC_047559.1\t141751\t141753\n", "NC_047559.1\t141777\t141779\n", "NC_047559.1\t268073\t268075\n", "NC_047559.1\t335756\t335758\n", "\n", "==> zr3644_19_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-upstreamFlanks <==\n", "NC_047559.1\t8970\t8972\n", "NC_047559.1\t8979\t8981\n", "NC_047559.1\t9159\t9161\n", "NC_047559.1\t9664\t9666\n", "NC_047559.1\t9774\t9776\n", "NC_047559.1\t9781\t9783\n", "NC_047559.1\t9787\t9789\n", "NC_047559.1\t9795\t9797\n", "NC_047559.1\t9803\t9805\n", "NC_047559.1\t9817\t9819\n", "\n", "==> zr3644_1_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-upstreamFlanks <==\n", "NC_047559.1\t9122\t9124\n", "NC_047559.1\t576634\t576636\n", "NC_047559.1\t576693\t576695\n", "NC_047559.1\t576752\t576754\n", "NC_047559.1\t3819453\t3819455\n", "NC_047559.1\t3819925\t3819927\n", "NC_047559.1\t3819934\t3819936\n", "NC_047559.1\t3819939\t3819941\n", "NC_047559.1\t3819941\t3819943\n", "NC_047559.1\t6312297\t6312299\n", "\n", "==> zr3644_1_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-upstreamFlanks <==\n", "NC_047559.1\t9140\t9142\n", "NC_047559.1\t9159\t9161\n", "NC_047559.1\t9240\t9242\n", "NC_047559.1\t268475\t268477\n", "NC_047559.1\t452984\t452986\n", "NC_047559.1\t471604\t471606\n", "NC_047559.1\t702986\t702988\n", "NC_047559.1\t785163\t785165\n", "NC_047559.1\t966292\t966294\n", "NC_047559.1\t966295\t966297\n", "\n", "==> zr3644_1_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-upstreamFlanks <==\n", "NC_047559.1\t9237\t9239\n", "NC_047559.1\t9774\t9776\n", "NC_047559.1\t9781\t9783\n", "NC_047559.1\t9787\t9789\n", "NC_047559.1\t9795\t9797\n", "NC_047559.1\t9803\t9805\n", "NC_047559.1\t9817\t9819\n", "NC_047559.1\t13113\t13115\n", "NC_047559.1\t13156\t13158\n", "NC_047559.1\t13182\t13184\n", "\n", "==> zr3644_20_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-upstreamFlanks <==\n", "NC_047559.1\t576308\t576310\n", "NC_047559.1\t576634\t576636\n", "NC_047559.1\t576693\t576695\n", "NC_047559.1\t576752\t576754\n", "NC_047559.1\t1419849\t1419851\n", "NC_047559.1\t1419877\t1419879\n", "NC_047559.1\t1419893\t1419895\n", "NC_047559.1\t1801087\t1801089\n", "NC_047559.1\t1801099\t1801101\n", "NC_047559.1\t1801111\t1801113\n", "\n", "==> zr3644_20_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-upstreamFlanks <==\n", "NC_047559.1\t8970\t8972\n", "NC_047559.1\t8979\t8981\n", "NC_047559.1\t335892\t335894\n", "NC_047559.1\t335912\t335914\n", "NC_047559.1\t335932\t335934\n", "NC_047559.1\t335960\t335962\n", "NC_047559.1\t335975\t335977\n", "NC_047559.1\t702986\t702988\n", "NC_047559.1\t778819\t778821\n", "NC_047559.1\t784804\t784806\n", "\n", "==> zr3644_20_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-upstreamFlanks <==\n", "NC_047559.1\t9122\t9124\n", "NC_047559.1\t9140\t9142\n", "NC_047559.1\t9159\t9161\n", "NC_047559.1\t9237\t9239\n", "NC_047559.1\t9240\t9242\n", "NC_047559.1\t9774\t9776\n", "NC_047559.1\t9781\t9783\n", "NC_047559.1\t9787\t9789\n", "NC_047559.1\t9795\t9797\n", "NC_047559.1\t9803\t9805\n", "\n", "==> zr3644_21_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-upstreamFlanks <==\n", "NC_047559.1\t141853\t141855\n", "NC_047559.1\t141858\t141860\n", "NC_047559.1\t142447\t142449\n", "NC_047559.1\t142465\t142467\n", "NC_047559.1\t142484\t142486\n", "NC_047559.1\t576308\t576310\n", "NC_047559.1\t576634\t576636\n", "NC_047559.1\t576693\t576695\n", "NC_047559.1\t576752\t576754\n", "NC_047559.1\t2190095\t2190097\n", "\n", "==> zr3644_21_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-upstreamFlanks <==\n", "NC_047559.1\t8970\t8972\n", "NC_047559.1\t8979\t8981\n", "NC_047559.1\t9122\t9124\n", "NC_047559.1\t9140\t9142\n", "NC_047559.1\t9237\t9239\n", "NC_047559.1\t9240\t9242\n", "NC_047559.1\t13475\t13477\n", "NC_047559.1\t79757\t79759\n", "NC_047559.1\t141605\t141607\n", "NC_047559.1\t141638\t141640\n", "\n", "==> zr3644_21_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-upstreamFlanks <==\n", "NC_047559.1\t9159\t9161\n", "NC_047559.1\t9774\t9776\n", "NC_047559.1\t9781\t9783\n", "NC_047559.1\t9787\t9789\n", "NC_047559.1\t9795\t9797\n", "NC_047559.1\t9803\t9805\n", "NC_047559.1\t9817\t9819\n", "NC_047559.1\t13113\t13115\n", "NC_047559.1\t13156\t13158\n", "NC_047559.1\t13182\t13184\n", "\n", "==> zr3644_22_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-upstreamFlanks <==\n", "NC_047559.1\t141708\t141710\n", "NC_047559.1\t141751\t141753\n", "NC_047559.1\t141777\t141779\n", "NC_047559.1\t576308\t576310\n", "NC_047559.1\t576634\t576636\n", "NC_047559.1\t576693\t576695\n", "NC_047559.1\t576752\t576754\n", "NC_047559.1\t3158566\t3158568\n", "NC_047559.1\t3763834\t3763836\n", "NC_047559.1\t3763866\t3763868\n", "\n", "==> zr3644_22_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-upstreamFlanks <==\n", "NC_047559.1\t9122\t9124\n", "NC_047559.1\t9140\t9142\n", "NC_047559.1\t9159\t9161\n", "NC_047559.1\t9237\t9239\n", "NC_047559.1\t9795\t9797\n", "NC_047559.1\t9803\t9805\n", "NC_047559.1\t141717\t141719\n", "NC_047559.1\t141800\t141802\n", "NC_047559.1\t335960\t335962\n", "NC_047559.1\t335975\t335977\n", "\n", "==> zr3644_22_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-upstreamFlanks <==\n", "NC_047559.1\t8979\t8981\n", "NC_047559.1\t9240\t9242\n", "NC_047559.1\t9774\t9776\n", "NC_047559.1\t9781\t9783\n", "NC_047559.1\t9787\t9789\n", "NC_047559.1\t9817\t9819\n", "NC_047559.1\t13156\t13158\n", "NC_047559.1\t13182\t13184\n", "NC_047559.1\t13186\t13188\n", "NC_047559.1\t13194\t13196\n", "\n", "==> zr3644_23_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-upstreamFlanks <==\n", "NC_047559.1\t576634\t576636\n", "NC_047559.1\t576693\t576695\n", "NC_047559.1\t3158461\t3158463\n", "NC_047559.1\t3158489\t3158491\n", "NC_047559.1\t3158542\t3158544\n", "NC_047559.1\t4539424\t4539426\n", "NC_047559.1\t4539447\t4539449\n", "NC_047559.1\t4539455\t4539457\n", "NC_047559.1\t4539514\t4539516\n", "NC_047559.1\t4952153\t4952155\n", "\n", "==> zr3644_23_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-upstreamFlanks <==\n", "NC_047559.1\t8979\t8981\n", "NC_047559.1\t9122\t9124\n", "NC_047559.1\t9140\t9142\n", "NC_047559.1\t9159\t9161\n", "NC_047559.1\t141708\t141710\n", "NC_047559.1\t141717\t141719\n", "NC_047559.1\t141751\t141753\n", "NC_047559.1\t141777\t141779\n", "NC_047559.1\t141800\t141802\n", "NC_047559.1\t141853\t141855\n", "\n", "==> zr3644_23_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-upstreamFlanks <==\n", "NC_047559.1\t8970\t8972\n", "NC_047559.1\t9237\t9239\n", "NC_047559.1\t9240\t9242\n", "NC_047559.1\t9774\t9776\n", "NC_047559.1\t9781\t9783\n", "NC_047559.1\t9787\t9789\n", "NC_047559.1\t9795\t9797\n", "NC_047559.1\t9803\t9805\n", "NC_047559.1\t9817\t9819\n", "NC_047559.1\t13113\t13115\n", "\n", "==> zr3644_24_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-upstreamFlanks <==\n", "NC_047559.1\t141708\t141710\n", "NC_047559.1\t141717\t141719\n", "NC_047559.1\t141751\t141753\n", "NC_047559.1\t141777\t141779\n", "NC_047559.1\t141800\t141802\n", "NC_047559.1\t576308\t576310\n", "NC_047559.1\t576634\t576636\n", "NC_047559.1\t576693\t576695\n", "NC_047559.1\t576752\t576754\n", "NC_047559.1\t3158461\t3158463\n", "\n", "==> zr3644_24_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-upstreamFlanks <==\n", "NC_047559.1\t8979\t8981\n", "NC_047559.1\t9122\t9124\n", "NC_047559.1\t9140\t9142\n", "NC_047559.1\t9159\t9161\n", "NC_047559.1\t9237\t9239\n", "NC_047559.1\t9240\t9242\n", "NC_047559.1\t9664\t9666\n", "NC_047559.1\t328531\t328533\n", "NC_047559.1\t354814\t354816\n", "NC_047559.1\t703222\t703224\n", "\n", "==> zr3644_24_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-upstreamFlanks <==\n", "NC_047559.1\t8970\t8972\n", "NC_047559.1\t9774\t9776\n", "NC_047559.1\t9781\t9783\n", "NC_047559.1\t9787\t9789\n", "NC_047559.1\t9795\t9797\n", "NC_047559.1\t9803\t9805\n", "NC_047559.1\t9817\t9819\n", "NC_047559.1\t13113\t13115\n", "NC_047559.1\t13156\t13158\n", "NC_047559.1\t13182\t13184\n", "\n", "==> zr3644_2_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-upstreamFlanks <==\n", "NC_047559.1\t576308\t576310\n", "NC_047559.1\t576634\t576636\n", "NC_047559.1\t576693\t576695\n", "NC_047559.1\t2190175\t2190177\n", "NC_047559.1\t2190215\t2190217\n", "NC_047559.1\t3819925\t3819927\n", "NC_047559.1\t3819934\t3819936\n", "NC_047559.1\t3819939\t3819941\n", "NC_047559.1\t3819941\t3819943\n", "NC_047559.1\t4951966\t4951968\n", "\n", "==> zr3644_2_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-upstreamFlanks <==\n", "NC_047559.1\t8970\t8972\n", "NC_047559.1\t8979\t8981\n", "NC_047559.1\t9122\t9124\n", "NC_047559.1\t9237\t9239\n", "NC_047559.1\t151725\t151727\n", "NC_047559.1\t268575\t268577\n", "NC_047559.1\t703439\t703441\n", "NC_047559.1\t857884\t857886\n", "NC_047559.1\t966782\t966784\n", "NC_047559.1\t1101302\t1101304\n", "\n", "==> zr3644_2_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-upstreamFlanks <==\n", "NC_047559.1\t9140\t9142\n", "NC_047559.1\t9159\t9161\n", "NC_047559.1\t9240\t9242\n", "NC_047559.1\t9774\t9776\n", "NC_047559.1\t9781\t9783\n", "NC_047559.1\t9787\t9789\n", "NC_047559.1\t9795\t9797\n", "NC_047559.1\t9803\t9805\n", "NC_047559.1\t9817\t9819\n", "NC_047559.1\t13156\t13158\n", "\n", "==> zr3644_3_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-upstreamFlanks <==\n", "NC_047559.1\t576634\t576636\n", "NC_047559.1\t576693\t576695\n", "NC_047559.1\t576752\t576754\n", "NC_047559.1\t3907322\t3907324\n", "NC_047559.1\t4952153\t4952155\n", "NC_047559.1\t4952182\t4952184\n", "NC_047559.1\t4952187\t4952189\n", "NC_047559.1\t5320440\t5320442\n", "NC_047559.1\t5320451\t5320453\n", "NC_047559.1\t6312459\t6312461\n", "\n", "==> zr3644_3_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-upstreamFlanks <==\n", "NC_047559.1\t8970\t8972\n", "NC_047559.1\t8979\t8981\n", "NC_047559.1\t9122\t9124\n", "NC_047559.1\t9140\t9142\n", "NC_047559.1\t9159\t9161\n", "NC_047559.1\t9781\t9783\n", "NC_047559.1\t9803\t9805\n", "NC_047559.1\t335850\t335852\n", "NC_047559.1\t335858\t335860\n", "NC_047559.1\t335878\t335880\n", "\n", "==> zr3644_3_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-upstreamFlanks <==\n", "NC_047559.1\t9237\t9239\n", "NC_047559.1\t9240\t9242\n", "NC_047559.1\t9774\t9776\n", "NC_047559.1\t9787\t9789\n", "NC_047559.1\t9795\t9797\n", "NC_047559.1\t9817\t9819\n", "NC_047559.1\t13113\t13115\n", "NC_047559.1\t13156\t13158\n", "NC_047559.1\t13182\t13184\n", "NC_047559.1\t13186\t13188\n", "\n", "==> zr3644_4_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-upstreamFlanks <==\n", "NC_047559.1\t9122\t9124\n", "NC_047559.1\t575861\t575863\n", "NC_047559.1\t576308\t576310\n", "NC_047559.1\t576634\t576636\n", "NC_047559.1\t576693\t576695\n", "NC_047559.1\t576752\t576754\n", "NC_047559.1\t3158542\t3158544\n", "NC_047559.1\t3158566\t3158568\n", "NC_047559.1\t3695107\t3695109\n", "NC_047559.1\t3919315\t3919317\n", "\n", "==> zr3644_4_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-upstreamFlanks <==\n", "NC_047559.1\t8970\t8972\n", "NC_047559.1\t8979\t8981\n", "NC_047559.1\t9140\t9142\n", "NC_047559.1\t9159\t9161\n", "NC_047559.1\t9237\t9239\n", "NC_047559.1\t254485\t254487\n", "NC_047559.1\t268601\t268603\n", "NC_047559.1\t335850\t335852\n", "NC_047559.1\t335858\t335860\n", "NC_047559.1\t335878\t335880\n", "\n", "==> zr3644_4_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-upstreamFlanks <==\n", "NC_047559.1\t9240\t9242\n", "NC_047559.1\t9774\t9776\n", "NC_047559.1\t9781\t9783\n", "NC_047559.1\t9787\t9789\n", "NC_047559.1\t9795\t9797\n", "NC_047559.1\t9803\t9805\n", "NC_047559.1\t9817\t9819\n", "NC_047559.1\t13182\t13184\n", "NC_047559.1\t13186\t13188\n", "NC_047559.1\t13194\t13196\n", "\n", "==> zr3644_5_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-upstreamFlanks <==\n", "NC_047559.1\t141717\t141719\n", "NC_047559.1\t141751\t141753\n", "NC_047559.1\t141777\t141779\n", "NC_047559.1\t141800\t141802\n", "NC_047559.1\t141853\t141855\n", "NC_047559.1\t141939\t141941\n", "NC_047559.1\t142371\t142373\n", "NC_047559.1\t142406\t142408\n", "NC_047559.1\t142411\t142413\n", "NC_047559.1\t142424\t142426\n", "\n", "==> zr3644_5_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-upstreamFlanks <==\n", "NC_047559.1\t9122\t9124\n", "NC_047559.1\t9140\t9142\n", "NC_047559.1\t9664\t9666\n", "NC_047559.1\t141708\t141710\n", "NC_047559.1\t141921\t141923\n", "NC_047559.1\t254396\t254398\n", "NC_047559.1\t328453\t328455\n", "NC_047559.1\t335756\t335758\n", "NC_047559.1\t335850\t335852\n", "NC_047559.1\t335858\t335860\n", "\n", "==> zr3644_5_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-upstreamFlanks <==\n", "NC_047559.1\t8970\t8972\n", "NC_047559.1\t8979\t8981\n", "NC_047559.1\t9159\t9161\n", "NC_047559.1\t9237\t9239\n", "NC_047559.1\t9240\t9242\n", "NC_047559.1\t9661\t9663\n", "NC_047559.1\t9774\t9776\n", "NC_047559.1\t9781\t9783\n", "NC_047559.1\t9787\t9789\n", "NC_047559.1\t9795\t9797\n", "\n", "==> zr3644_6_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-upstreamFlanks <==\n", "NC_047559.1\t142406\t142408\n", "NC_047559.1\t142411\t142413\n", "NC_047559.1\t142424\t142426\n", "NC_047559.1\t142447\t142449\n", "NC_047559.1\t142451\t142453\n", "NC_047559.1\t142465\t142467\n", "NC_047559.1\t142484\t142486\n", "NC_047559.1\t142490\t142492\n", "NC_047559.1\t142504\t142506\n", "NC_047559.1\t576308\t576310\n", "\n", "==> zr3644_6_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-upstreamFlanks <==\n", "NC_047559.1\t8970\t8972\n", "NC_047559.1\t8979\t8981\n", "NC_047559.1\t9122\t9124\n", "NC_047559.1\t9140\t9142\n", "NC_047559.1\t9159\t9161\n", "NC_047559.1\t9661\t9663\n", "NC_047559.1\t141708\t141710\n", "NC_047559.1\t141717\t141719\n", "NC_047559.1\t141751\t141753\n", "NC_047559.1\t141777\t141779\n", "\n", "==> zr3644_6_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-upstreamFlanks <==\n", "NC_047559.1\t9237\t9239\n", "NC_047559.1\t9240\t9242\n", "NC_047559.1\t9658\t9660\n", "NC_047559.1\t9664\t9666\n", "NC_047559.1\t9774\t9776\n", "NC_047559.1\t9781\t9783\n", "NC_047559.1\t9787\t9789\n", "NC_047559.1\t9795\t9797\n", "NC_047559.1\t9803\t9805\n", "NC_047559.1\t9817\t9819\n", "\n", "==> zr3644_7_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-upstreamFlanks <==\n", "NC_047559.1\t141777\t141779\n", "NC_047559.1\t141800\t141802\n", "NC_047559.1\t141868\t141870\n", "NC_047559.1\t141888\t141890\n", "NC_047559.1\t141905\t141907\n", "NC_047559.1\t142357\t142359\n", "NC_047559.1\t142371\t142373\n", "NC_047559.1\t142406\t142408\n", "NC_047559.1\t142411\t142413\n", "NC_047559.1\t142424\t142426\n", "\n", "==> zr3644_7_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-upstreamFlanks <==\n", "NC_047559.1\t8970\t8972\n", "NC_047559.1\t8979\t8981\n", "NC_047559.1\t9122\t9124\n", "NC_047559.1\t9140\t9142\n", "NC_047559.1\t9159\t9161\n", "NC_047559.1\t13643\t13645\n", "NC_047559.1\t141708\t141710\n", "NC_047559.1\t141717\t141719\n", "NC_047559.1\t141751\t141753\n", "NC_047559.1\t141853\t141855\n", "\n", "==> zr3644_7_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-upstreamFlanks <==\n", "NC_047559.1\t9237\t9239\n", "NC_047559.1\t9240\t9242\n", "NC_047559.1\t9658\t9660\n", "NC_047559.1\t9664\t9666\n", "NC_047559.1\t9774\t9776\n", "NC_047559.1\t9781\t9783\n", "NC_047559.1\t9787\t9789\n", "NC_047559.1\t9795\t9797\n", "NC_047559.1\t9803\t9805\n", "NC_047559.1\t9817\t9819\n", "\n", "==> zr3644_8_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-upstreamFlanks <==\n", "NC_047559.1\t576634\t576636\n", "NC_047559.1\t576693\t576695\n", "NC_047559.1\t576752\t576754\n", "NC_047559.1\t3837935\t3837937\n", "NC_047559.1\t4539374\t4539376\n", "NC_047559.1\t4539396\t4539398\n", "NC_047559.1\t4539424\t4539426\n", "NC_047559.1\t4539447\t4539449\n", "NC_047559.1\t4952222\t4952224\n", "NC_047559.1\t5320354\t5320356\n", "\n", "==> zr3644_8_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-upstreamFlanks <==\n", "NC_047559.1\t8970\t8972\n", "NC_047559.1\t8979\t8981\n", "NC_047559.1\t9122\t9124\n", "NC_047559.1\t9140\t9142\n", "NC_047559.1\t9795\t9797\n", "NC_047559.1\t335850\t335852\n", "NC_047559.1\t335858\t335860\n", "NC_047559.1\t335878\t335880\n", "NC_047559.1\t335886\t335888\n", "NC_047559.1\t702986\t702988\n", "\n", "==> zr3644_8_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-upstreamFlanks <==\n", "NC_047559.1\t9159\t9161\n", "NC_047559.1\t9237\t9239\n", "NC_047559.1\t9240\t9242\n", "NC_047559.1\t9774\t9776\n", "NC_047559.1\t9781\t9783\n", "NC_047559.1\t9787\t9789\n", "NC_047559.1\t9803\t9805\n", "NC_047559.1\t9817\t9819\n", "NC_047559.1\t13113\t13115\n", "NC_047559.1\t13156\t13158\n", "\n", "==> zr3644_9_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-upstreamFlanks <==\n", "NC_047559.1\t141751\t141753\n", "NC_047559.1\t141777\t141779\n", "NC_047559.1\t141800\t141802\n", "NC_047559.1\t142406\t142408\n", "NC_047559.1\t142411\t142413\n", "NC_047559.1\t142424\t142426\n", "NC_047559.1\t142504\t142506\n", "NC_047559.1\t576308\t576310\n", "NC_047559.1\t576634\t576636\n", "NC_047559.1\t576693\t576695\n", "\n", "==> zr3644_9_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-upstreamFlanks <==\n", "NC_047559.1\t8970\t8972\n", "NC_047559.1\t9122\t9124\n", "NC_047559.1\t9774\t9776\n", "NC_047559.1\t9781\t9783\n", "NC_047559.1\t9787\t9789\n", "NC_047559.1\t9795\t9797\n", "NC_047559.1\t9803\t9805\n", "NC_047559.1\t335850\t335852\n", "NC_047559.1\t335858\t335860\n", "NC_047559.1\t335886\t335888\n", "\n", "==> zr3644_9_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-upstreamFlanks <==\n", "NC_047559.1\t8979\t8981\n", "NC_047559.1\t9140\t9142\n", "NC_047559.1\t9159\t9161\n", "NC_047559.1\t9817\t9819\n", "NC_047559.1\t13156\t13158\n", "NC_047559.1\t13182\t13184\n", "NC_047559.1\t13186\t13188\n", "NC_047559.1\t13194\t13196\n", "NC_047559.1\t13216\t13218\n", "NC_047559.1\t13262\t13264\n", "\n", "==> zr3644_union-averages_5x.bedgraph-Meth.bed-upstreamFlanks <==\n", "NC_047559.1\t141853\t141855\n", "NC_047559.1\t141939\t141941\n", "NC_047559.1\t142406\t142408\n", "NC_047559.1\t142411\t142413\n", "NC_047559.1\t142424\t142426\n", "NC_047559.1\t142447\t142449\n", "NC_047559.1\t142451\t142453\n", "NC_047559.1\t576308\t576310\n", "NC_047559.1\t576634\t576636\n", "NC_047559.1\t576693\t576695\n", "\n", "==> zr3644_union-averages_5x.bedgraph-sparseMeth.bed-upstreamFlanks <==\n", "NC_047559.1\t8970\t8972\n", "NC_047559.1\t8979\t8981\n", "NC_047559.1\t9122\t9124\n", "NC_047559.1\t9140\t9142\n", "NC_047559.1\t9159\t9161\n", "NC_047559.1\t9603\t9605\n", "NC_047559.1\t141708\t141710\n", "NC_047559.1\t141717\t141719\n", "NC_047559.1\t141751\t141753\n", "NC_047559.1\t141777\t141779\n", "\n", "==> zr3644_union-averages_5x.bedgraph-unMeth.bed-upstreamFlanks <==\n", "NC_047559.1\t9237\t9239\n", "NC_047559.1\t9240\t9242\n", "NC_047559.1\t9658\t9660\n", "NC_047559.1\t9661\t9663\n", "NC_047559.1\t9664\t9666\n", "NC_047559.1\t9774\t9776\n", "NC_047559.1\t9781\t9783\n", "NC_047559.1\t9787\t9789\n", "NC_047559.1\t9795\t9797\n", "NC_047559.1\t9803\t9805\n" ] } ], "source": [ "#Check output\n", "!head *upstreamFlanks" ] }, { "cell_type": "code", "execution_count": 77, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ " 3277 zr3644_10_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-upstreamFlanks\n", " 13144 zr3644_10_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-upstreamFlanks\n", " 281363 zr3644_10_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-upstreamFlanks\n", " 3423 zr3644_11_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-upstreamFlanks\n", " 13735 zr3644_11_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-upstreamFlanks\n", " 296613 zr3644_11_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-upstreamFlanks\n", " 2942 zr3644_12_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-upstreamFlanks\n", " 12111 zr3644_12_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-upstreamFlanks\n", " 275129 zr3644_12_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-upstreamFlanks\n", " 3314 zr3644_13_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-upstreamFlanks\n", " 13439 zr3644_13_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-upstreamFlanks\n", " 293489 zr3644_13_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-upstreamFlanks\n", " 3174 zr3644_14_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-upstreamFlanks\n", " 9898 zr3644_14_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-upstreamFlanks\n", " 225482 zr3644_14_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-upstreamFlanks\n", " 3815 zr3644_15_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-upstreamFlanks\n", " 13916 zr3644_15_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-upstreamFlanks\n", " 307670 zr3644_15_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-upstreamFlanks\n", " 3010 zr3644_16_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-upstreamFlanks\n", " 12282 zr3644_16_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-upstreamFlanks\n", " 267399 zr3644_16_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-upstreamFlanks\n", " 3456 zr3644_17_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-upstreamFlanks\n", " 11903 zr3644_17_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-upstreamFlanks\n", " 289533 zr3644_17_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-upstreamFlanks\n", " 3130 zr3644_18_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-upstreamFlanks\n", " 12961 zr3644_18_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-upstreamFlanks\n", " 278879 zr3644_18_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-upstreamFlanks\n", " 2957 zr3644_19_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-upstreamFlanks\n", " 12269 zr3644_19_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-upstreamFlanks\n", " 275117 zr3644_19_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-upstreamFlanks\n", " 2721 zr3644_1_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-upstreamFlanks\n", " 11522 zr3644_1_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-upstreamFlanks\n", " 268952 zr3644_1_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-upstreamFlanks\n", " 3200 zr3644_20_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-upstreamFlanks\n", " 13127 zr3644_20_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-upstreamFlanks\n", " 289350 zr3644_20_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-upstreamFlanks\n", " 3178 zr3644_21_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-upstreamFlanks\n", " 13061 zr3644_21_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-upstreamFlanks\n", " 286100 zr3644_21_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-upstreamFlanks\n", " 2985 zr3644_22_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-upstreamFlanks\n", " 11952 zr3644_22_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-upstreamFlanks\n", " 266121 zr3644_22_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-upstreamFlanks\n", " 2424 zr3644_23_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-upstreamFlanks\n", " 11022 zr3644_23_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-upstreamFlanks\n", " 234334 zr3644_23_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-upstreamFlanks\n", " 3074 zr3644_24_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-upstreamFlanks\n", " 12525 zr3644_24_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-upstreamFlanks\n", " 284763 zr3644_24_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-upstreamFlanks\n", " 3594 zr3644_2_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-upstreamFlanks\n", " 11932 zr3644_2_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-upstreamFlanks\n", " 295926 zr3644_2_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-upstreamFlanks\n", " 2616 zr3644_3_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-upstreamFlanks\n", " 11460 zr3644_3_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-upstreamFlanks\n", " 235857 zr3644_3_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-upstreamFlanks\n", " 3051 zr3644_4_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-upstreamFlanks\n", " 12470 zr3644_4_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-upstreamFlanks\n", " 278324 zr3644_4_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-upstreamFlanks\n", " 2793 zr3644_5_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-upstreamFlanks\n", " 12417 zr3644_5_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-upstreamFlanks\n", " 259856 zr3644_5_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-upstreamFlanks\n", " 3067 zr3644_6_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-upstreamFlanks\n", " 13095 zr3644_6_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-upstreamFlanks\n", " 289649 zr3644_6_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-upstreamFlanks\n", " 4233 zr3644_7_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-upstreamFlanks\n", " 15735 zr3644_7_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-upstreamFlanks\n", " 357361 zr3644_7_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-upstreamFlanks\n", " 2797 zr3644_8_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-upstreamFlanks\n", " 11907 zr3644_8_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-upstreamFlanks\n", " 248390 zr3644_8_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-upstreamFlanks\n", " 2963 zr3644_9_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-upstreamFlanks\n", " 12219 zr3644_9_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-upstreamFlanks\n", " 252413 zr3644_9_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-upstreamFlanks\n", " 4683 zr3644_union-averages_5x.bedgraph-Meth.bed-upstreamFlanks\n", " 17767 zr3644_union-averages_5x.bedgraph-sparseMeth.bed-upstreamFlanks\n", " 463665 zr3644_union-averages_5x.bedgraph-unMeth.bed-upstreamFlanks\n", " 7499481 total\n" ] } ], "source": [ "#Count number of overlaps\n", "!wc -l *upstreamFlanks" ] }, { "cell_type": "code", "execution_count": 78, "metadata": { "collapsed": true }, "outputs": [], "source": [ "#Get line counts for each fine\n", "# Remove 28th line (total entries)\n", "#Ensure output is tab-delimited\n", "#Save output\n", "!wc -l *-upstreamFlanks \\\n", "| sed '76,$ d' \\\n", "| awk '{print $1\"\\t\"$2}' \\\n", "> zr3644_5x-upstreamFlanks-counts.txt" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "### 6g. Downstream flanks" ] }, { "cell_type": "code", "execution_count": 59, "metadata": { "collapsed": false }, "outputs": [], "source": [ "%%bash\n", "for f in *bed\n", "do\n", " /Users/Shared/bioinformatics/bedtools2/bin/intersectBed \\\n", " -u \\\n", " -a ${f} \\\n", " -b /Volumes/web-1/halfshell/genomic-databank/cgigas_uk_roslin_v1_downstream.gff \\\n", " > ${f}-downstreamFlanks\n", "done" ] }, { "cell_type": "code", "execution_count": 60, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "==> zr3644_10_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-downstreamFlanks <==\n", "NC_047559.1\t344549\t344551\n", "NC_047559.1\t344803\t344805\n", "NC_047559.1\t344812\t344814\n", "NC_047559.1\t344972\t344974\n", "NC_047559.1\t344976\t344978\n", "NC_047559.1\t434252\t434254\n", "NC_047559.1\t434266\t434268\n", "NC_047559.1\t576634\t576636\n", "NC_047559.1\t576693\t576695\n", "NC_047559.1\t576752\t576754\n", "\n", "==> zr3644_10_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-downstreamFlanks <==\n", "NC_047559.1\t142484\t142486\n", "NC_047559.1\t142531\t142533\n", "NC_047559.1\t142545\t142547\n", "NC_047559.1\t142593\t142595\n", "NC_047559.1\t258248\t258250\n", "NC_047559.1\t325786\t325788\n", "NC_047559.1\t325842\t325844\n", "NC_047559.1\t344623\t344625\n", "NC_047559.1\t344785\t344787\n", "NC_047559.1\t344794\t344796\n", "\n", "==> zr3644_10_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-downstreamFlanks <==\n", "NC_047559.1\t16061\t16063\n", "NC_047559.1\t16105\t16107\n", "NC_047559.1\t16112\t16114\n", "NC_047559.1\t16220\t16222\n", "NC_047559.1\t16260\t16262\n", "NC_047559.1\t16289\t16291\n", "NC_047559.1\t16310\t16312\n", "NC_047559.1\t16369\t16371\n", "NC_047559.1\t16409\t16411\n", "NC_047559.1\t16438\t16440\n", "\n", "==> zr3644_11_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-downstreamFlanks <==\n", "NC_047559.1\t142406\t142408\n", "NC_047559.1\t142411\t142413\n", "NC_047559.1\t142424\t142426\n", "NC_047559.1\t142447\t142449\n", "NC_047559.1\t142451\t142453\n", "NC_047559.1\t142465\t142467\n", "NC_047559.1\t142484\t142486\n", "NC_047559.1\t142531\t142533\n", "NC_047559.1\t142545\t142547\n", "NC_047559.1\t142593\t142595\n", "\n", "==> zr3644_11_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-downstreamFlanks <==\n", "NC_047559.1\t142504\t142506\n", "NC_047559.1\t264885\t264887\n", "NC_047559.1\t264911\t264913\n", "NC_047559.1\t264924\t264926\n", "NC_047559.1\t264959\t264961\n", "NC_047559.1\t265013\t265015\n", "NC_047559.1\t265028\t265030\n", "NC_047559.1\t344549\t344551\n", "NC_047559.1\t344623\t344625\n", "NC_047559.1\t344861\t344863\n", "\n", "==> zr3644_11_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-downstreamFlanks <==\n", "NC_047559.1\t12229\t12231\n", "NC_047559.1\t12254\t12256\n", "NC_047559.1\t16061\t16063\n", "NC_047559.1\t16105\t16107\n", "NC_047559.1\t16112\t16114\n", "NC_047559.1\t16220\t16222\n", "NC_047559.1\t16260\t16262\n", "NC_047559.1\t16289\t16291\n", "NC_047559.1\t16310\t16312\n", "NC_047559.1\t16369\t16371\n", "\n", "==> zr3644_12_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-downstreamFlanks <==\n", "NC_047559.1\t434252\t434254\n", "NC_047559.1\t434266\t434268\n", "NC_047559.1\t576634\t576636\n", "NC_047559.1\t576693\t576695\n", "NC_047559.1\t576752\t576754\n", "NC_047559.1\t576866\t576868\n", "NC_047559.1\t576880\t576882\n", "NC_047559.1\t576914\t576916\n", "NC_047559.1\t577456\t577458\n", "NC_047559.1\t1010121\t1010123\n", "\n", "==> zr3644_12_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-downstreamFlanks <==\n", "NC_047559.1\t16856\t16858\n", "NC_047559.1\t142531\t142533\n", "NC_047559.1\t142545\t142547\n", "NC_047559.1\t142689\t142691\n", "NC_047559.1\t264885\t264887\n", "NC_047559.1\t264911\t264913\n", "NC_047559.1\t264924\t264926\n", "NC_047559.1\t264959\t264961\n", "NC_047559.1\t265013\t265015\n", "NC_047559.1\t265028\t265030\n", "\n", "==> zr3644_12_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-downstreamFlanks <==\n", "NC_047559.1\t16061\t16063\n", "NC_047559.1\t16105\t16107\n", "NC_047559.1\t16112\t16114\n", "NC_047559.1\t16220\t16222\n", "NC_047559.1\t16260\t16262\n", "NC_047559.1\t16289\t16291\n", "NC_047559.1\t16310\t16312\n", "NC_047559.1\t16369\t16371\n", "NC_047559.1\t16409\t16411\n", "NC_047559.1\t16438\t16440\n", "\n", "==> zr3644_13_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-downstreamFlanks <==\n", "NC_047559.1\t576634\t576636\n", "NC_047559.1\t576693\t576695\n", "NC_047559.1\t576752\t576754\n", "NC_047559.1\t576866\t576868\n", "NC_047559.1\t576880\t576882\n", "NC_047559.1\t576914\t576916\n", "NC_047559.1\t577456\t577458\n", "NC_047559.1\t1010121\t1010123\n", "NC_047559.1\t1010136\t1010138\n", "NC_047559.1\t1010303\t1010305\n", "\n", "==> zr3644_13_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-downstreamFlanks <==\n", "NC_047559.1\t142484\t142486\n", "NC_047559.1\t142490\t142492\n", "NC_047559.1\t142531\t142533\n", "NC_047559.1\t142545\t142547\n", "NC_047559.1\t142689\t142691\n", "NC_047559.1\t265013\t265015\n", "NC_047559.1\t265028\t265030\n", "NC_047559.1\t433584\t433586\n", "NC_047559.1\t433588\t433590\n", "NC_047559.1\t433598\t433600\n", "\n", "==> zr3644_13_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-downstreamFlanks <==\n", "NC_047559.1\t12229\t12231\n", "NC_047559.1\t12254\t12256\n", "NC_047559.1\t16061\t16063\n", "NC_047559.1\t16105\t16107\n", "NC_047559.1\t16112\t16114\n", "NC_047559.1\t16220\t16222\n", "NC_047559.1\t16260\t16262\n", "NC_047559.1\t16289\t16291\n", "NC_047559.1\t16310\t16312\n", "NC_047559.1\t16369\t16371\n", "\n", "==> zr3644_14_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-downstreamFlanks <==\n", "NC_047559.1\t344549\t344551\n", "NC_047559.1\t576634\t576636\n", "NC_047559.1\t576693\t576695\n", "NC_047559.1\t576752\t576754\n", "NC_047559.1\t576866\t576868\n", "NC_047559.1\t576880\t576882\n", "NC_047559.1\t576914\t576916\n", "NC_047559.1\t577456\t577458\n", "NC_047559.1\t1010136\t1010138\n", "NC_047559.1\t1010921\t1010923\n", "\n", "==> zr3644_14_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-downstreamFlanks <==\n", "NC_047559.1\t209926\t209928\n", "NC_047559.1\t326118\t326120\n", "NC_047559.1\t326295\t326297\n", "NC_047559.1\t326317\t326319\n", "NC_047559.1\t344623\t344625\n", "NC_047559.1\t344785\t344787\n", "NC_047559.1\t344794\t344796\n", "NC_047559.1\t344803\t344805\n", "NC_047559.1\t344812\t344814\n", "NC_047559.1\t344829\t344831\n", "\n", "==> zr3644_14_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-downstreamFlanks <==\n", "NC_047559.1\t16061\t16063\n", "NC_047559.1\t16105\t16107\n", "NC_047559.1\t16112\t16114\n", "NC_047559.1\t16220\t16222\n", "NC_047559.1\t16260\t16262\n", "NC_047559.1\t16289\t16291\n", "NC_047559.1\t16310\t16312\n", "NC_047559.1\t16369\t16371\n", "NC_047559.1\t16409\t16411\n", "NC_047559.1\t16438\t16440\n", "\n", "==> zr3644_15_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-downstreamFlanks <==\n", "NC_047559.1\t141853\t141855\n", "NC_047559.1\t141858\t141860\n", "NC_047559.1\t141894\t141896\n", "NC_047559.1\t142406\t142408\n", "NC_047559.1\t142411\t142413\n", "NC_047559.1\t142424\t142426\n", "NC_047559.1\t433584\t433586\n", "NC_047559.1\t433588\t433590\n", "NC_047559.1\t433598\t433600\n", "NC_047559.1\t576634\t576636\n", "\n", "==> zr3644_15_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-downstreamFlanks <==\n", "NC_047559.1\t142465\t142467\n", "NC_047559.1\t142484\t142486\n", "NC_047559.1\t142490\t142492\n", "NC_047559.1\t142504\t142506\n", "NC_047559.1\t142531\t142533\n", "NC_047559.1\t142545\t142547\n", "NC_047559.1\t142593\t142595\n", "NC_047559.1\t142689\t142691\n", "NC_047559.1\t229571\t229573\n", "NC_047559.1\t264885\t264887\n", "\n", "==> zr3644_15_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-downstreamFlanks <==\n", "NC_047559.1\t16061\t16063\n", "NC_047559.1\t16105\t16107\n", "NC_047559.1\t16112\t16114\n", "NC_047559.1\t16220\t16222\n", "NC_047559.1\t16260\t16262\n", "NC_047559.1\t16289\t16291\n", "NC_047559.1\t16310\t16312\n", "NC_047559.1\t16369\t16371\n", "NC_047559.1\t16409\t16411\n", "NC_047559.1\t16438\t16440\n", "\n", "==> zr3644_16_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-downstreamFlanks <==\n", "NC_047559.1\t344549\t344551\n", "NC_047559.1\t433598\t433600\n", "NC_047559.1\t576634\t576636\n", "NC_047559.1\t576693\t576695\n", "NC_047559.1\t576752\t576754\n", "NC_047559.1\t576866\t576868\n", "NC_047559.1\t576880\t576882\n", "NC_047559.1\t1010121\t1010123\n", "NC_047559.1\t1010136\t1010138\n", "NC_047559.1\t1010560\t1010562\n", "\n", "==> zr3644_16_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-downstreamFlanks <==\n", "NC_047559.1\t209971\t209973\n", "NC_047559.1\t265013\t265015\n", "NC_047559.1\t265028\t265030\n", "NC_047559.1\t265265\t265267\n", "NC_047559.1\t265353\t265355\n", "NC_047559.1\t344785\t344787\n", "NC_047559.1\t344794\t344796\n", "NC_047559.1\t344803\t344805\n", "NC_047559.1\t344812\t344814\n", "NC_047559.1\t344829\t344831\n", "\n", "==> zr3644_16_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-downstreamFlanks <==\n", "NC_047559.1\t16061\t16063\n", "NC_047559.1\t16105\t16107\n", "NC_047559.1\t16112\t16114\n", "NC_047559.1\t16220\t16222\n", "NC_047559.1\t16260\t16262\n", "NC_047559.1\t16289\t16291\n", "NC_047559.1\t16310\t16312\n", "NC_047559.1\t16369\t16371\n", "NC_047559.1\t16409\t16411\n", "NC_047559.1\t16438\t16440\n", "\n", "==> zr3644_17_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-downstreamFlanks <==\n", "NC_047559.1\t433584\t433586\n", "NC_047559.1\t433588\t433590\n", "NC_047559.1\t433598\t433600\n", "NC_047559.1\t576634\t576636\n", "NC_047559.1\t576693\t576695\n", "NC_047559.1\t576752\t576754\n", "NC_047559.1\t576866\t576868\n", "NC_047559.1\t576880\t576882\n", "NC_047559.1\t576914\t576916\n", "NC_047559.1\t577126\t577128\n", "\n", "==> zr3644_17_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-downstreamFlanks <==\n", "NC_047559.1\t142465\t142467\n", "NC_047559.1\t142484\t142486\n", "NC_047559.1\t142490\t142492\n", "NC_047559.1\t142504\t142506\n", "NC_047559.1\t142531\t142533\n", "NC_047559.1\t142545\t142547\n", "NC_047559.1\t142593\t142595\n", "NC_047559.1\t142689\t142691\n", "NC_047559.1\t142714\t142716\n", "NC_047559.1\t326295\t326297\n", "\n", "==> zr3644_17_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-downstreamFlanks <==\n", "NC_047559.1\t12229\t12231\n", "NC_047559.1\t12254\t12256\n", "NC_047559.1\t16061\t16063\n", "NC_047559.1\t16105\t16107\n", "NC_047559.1\t16112\t16114\n", "NC_047559.1\t16220\t16222\n", "NC_047559.1\t16260\t16262\n", "NC_047559.1\t16289\t16291\n", "NC_047559.1\t16310\t16312\n", "NC_047559.1\t16369\t16371\n", "\n", "==> zr3644_18_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-downstreamFlanks <==\n", "NC_047559.1\t142424\t142426\n", "NC_047559.1\t142447\t142449\n", "NC_047559.1\t142451\t142453\n", "NC_047559.1\t142465\t142467\n", "NC_047559.1\t576634\t576636\n", "NC_047559.1\t576693\t576695\n", "NC_047559.1\t576752\t576754\n", "NC_047559.1\t576866\t576868\n", "NC_047559.1\t576880\t576882\n", "NC_047559.1\t576914\t576916\n", "\n", "==> zr3644_18_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-downstreamFlanks <==\n", "NC_047559.1\t141853\t141855\n", "NC_047559.1\t141858\t141860\n", "NC_047559.1\t141868\t141870\n", "NC_047559.1\t141885\t141887\n", "NC_047559.1\t141888\t141890\n", "NC_047559.1\t141894\t141896\n", "NC_047559.1\t141905\t141907\n", "NC_047559.1\t141912\t141914\n", "NC_047559.1\t141921\t141923\n", "NC_047559.1\t142484\t142486\n", "\n", "==> zr3644_18_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-downstreamFlanks <==\n", "NC_047559.1\t16061\t16063\n", "NC_047559.1\t16105\t16107\n", "NC_047559.1\t16112\t16114\n", "NC_047559.1\t16220\t16222\n", "NC_047559.1\t16260\t16262\n", "NC_047559.1\t16289\t16291\n", "NC_047559.1\t16310\t16312\n", "NC_047559.1\t16369\t16371\n", "NC_047559.1\t16409\t16411\n", "NC_047559.1\t16438\t16440\n", "\n", "==> zr3644_19_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-downstreamFlanks <==\n", "NC_047559.1\t141853\t141855\n", "NC_047559.1\t141858\t141860\n", "NC_047559.1\t142531\t142533\n", "NC_047559.1\t142545\t142547\n", "NC_047559.1\t576634\t576636\n", "NC_047559.1\t576693\t576695\n", "NC_047559.1\t576752\t576754\n", "NC_047559.1\t576866\t576868\n", "NC_047559.1\t576880\t576882\n", "NC_047559.1\t577126\t577128\n", "\n", "==> zr3644_19_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-downstreamFlanks <==\n", "NC_047559.1\t12254\t12256\n", "NC_047559.1\t142593\t142595\n", "NC_047559.1\t325766\t325768\n", "NC_047559.1\t344829\t344831\n", "NC_047559.1\t344838\t344840\n", "NC_047559.1\t344861\t344863\n", "NC_047559.1\t344972\t344974\n", "NC_047559.1\t344976\t344978\n", "NC_047559.1\t344985\t344987\n", "NC_047559.1\t344987\t344989\n", "\n", "==> zr3644_19_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-downstreamFlanks <==\n", "NC_047559.1\t12229\t12231\n", "NC_047559.1\t16061\t16063\n", "NC_047559.1\t16105\t16107\n", "NC_047559.1\t16112\t16114\n", "NC_047559.1\t16220\t16222\n", "NC_047559.1\t16260\t16262\n", "NC_047559.1\t16289\t16291\n", "NC_047559.1\t16310\t16312\n", "NC_047559.1\t16369\t16371\n", "NC_047559.1\t16409\t16411\n", "\n", "==> zr3644_1_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-downstreamFlanks <==\n", "NC_047559.1\t576634\t576636\n", "NC_047559.1\t576693\t576695\n", "NC_047559.1\t576752\t576754\n", "NC_047559.1\t576866\t576868\n", "NC_047559.1\t576880\t576882\n", "NC_047559.1\t1010121\t1010123\n", "NC_047559.1\t1010757\t1010759\n", "NC_047559.1\t1010921\t1010923\n", "NC_047559.1\t1011065\t1011067\n", "NC_047559.1\t1170126\t1170128\n", "\n", "==> zr3644_1_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-downstreamFlanks <==\n", "NC_047559.1\t264911\t264913\n", "NC_047559.1\t264959\t264961\n", "NC_047559.1\t265111\t265113\n", "NC_047559.1\t326131\t326133\n", "NC_047559.1\t344549\t344551\n", "NC_047559.1\t344623\t344625\n", "NC_047559.1\t344785\t344787\n", "NC_047559.1\t344794\t344796\n", "NC_047559.1\t344803\t344805\n", "NC_047559.1\t344812\t344814\n", "\n", "==> zr3644_1_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-downstreamFlanks <==\n", "NC_047559.1\t16061\t16063\n", "NC_047559.1\t16105\t16107\n", "NC_047559.1\t16112\t16114\n", "NC_047559.1\t16220\t16222\n", "NC_047559.1\t16260\t16262\n", "NC_047559.1\t16289\t16291\n", "NC_047559.1\t16310\t16312\n", "NC_047559.1\t16369\t16371\n", "NC_047559.1\t16409\t16411\n", "NC_047559.1\t16438\t16440\n", "\n", "==> zr3644_20_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-downstreamFlanks <==\n", "NC_047559.1\t576634\t576636\n", "NC_047559.1\t576693\t576695\n", "NC_047559.1\t576752\t576754\n", "NC_047559.1\t576866\t576868\n", "NC_047559.1\t576880\t576882\n", "NC_047559.1\t577456\t577458\n", "NC_047559.1\t1010121\t1010123\n", "NC_047559.1\t1010136\t1010138\n", "NC_047559.1\t1010560\t1010562\n", "NC_047559.1\t1190116\t1190118\n", "\n", "==> zr3644_20_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-downstreamFlanks <==\n", "NC_047559.1\t264911\t264913\n", "NC_047559.1\t264924\t264926\n", "NC_047559.1\t264959\t264961\n", "NC_047559.1\t265013\t265015\n", "NC_047559.1\t265028\t265030\n", "NC_047559.1\t326072\t326074\n", "NC_047559.1\t344549\t344551\n", "NC_047559.1\t433584\t433586\n", "NC_047559.1\t433588\t433590\n", "NC_047559.1\t433598\t433600\n", "\n", "==> zr3644_20_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-downstreamFlanks <==\n", "NC_047559.1\t16061\t16063\n", "NC_047559.1\t16105\t16107\n", "NC_047559.1\t16112\t16114\n", "NC_047559.1\t16220\t16222\n", "NC_047559.1\t16260\t16262\n", "NC_047559.1\t16289\t16291\n", "NC_047559.1\t16310\t16312\n", "NC_047559.1\t16369\t16371\n", "NC_047559.1\t16409\t16411\n", "NC_047559.1\t16438\t16440\n", "\n", "==> zr3644_21_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-downstreamFlanks <==\n", "NC_047559.1\t141853\t141855\n", "NC_047559.1\t141858\t141860\n", "NC_047559.1\t142447\t142449\n", "NC_047559.1\t142465\t142467\n", "NC_047559.1\t142484\t142486\n", "NC_047559.1\t344549\t344551\n", "NC_047559.1\t433588\t433590\n", "NC_047559.1\t433598\t433600\n", "NC_047559.1\t433645\t433647\n", "NC_047559.1\t576634\t576636\n", "\n", "==> zr3644_21_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-downstreamFlanks <==\n", "NC_047559.1\t142490\t142492\n", "NC_047559.1\t142504\t142506\n", "NC_047559.1\t142531\t142533\n", "NC_047559.1\t142545\t142547\n", "NC_047559.1\t142593\t142595\n", "NC_047559.1\t264959\t264961\n", "NC_047559.1\t344623\t344625\n", "NC_047559.1\t344785\t344787\n", "NC_047559.1\t344794\t344796\n", "NC_047559.1\t344812\t344814\n", "\n", "==> zr3644_21_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-downstreamFlanks <==\n", "NC_047559.1\t16061\t16063\n", "NC_047559.1\t16105\t16107\n", "NC_047559.1\t16112\t16114\n", "NC_047559.1\t16220\t16222\n", "NC_047559.1\t16260\t16262\n", "NC_047559.1\t16289\t16291\n", "NC_047559.1\t16310\t16312\n", "NC_047559.1\t16369\t16371\n", "NC_047559.1\t16409\t16411\n", "NC_047559.1\t16438\t16440\n", "\n", "==> zr3644_22_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-downstreamFlanks <==\n", "NC_047559.1\t344440\t344442\n", "NC_047559.1\t344477\t344479\n", "NC_047559.1\t344803\t344805\n", "NC_047559.1\t344812\t344814\n", "NC_047559.1\t344829\t344831\n", "NC_047559.1\t344838\t344840\n", "NC_047559.1\t434252\t434254\n", "NC_047559.1\t434266\t434268\n", "NC_047559.1\t576634\t576636\n", "NC_047559.1\t576693\t576695\n", "\n", "==> zr3644_22_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-downstreamFlanks <==\n", "NC_047559.1\t344794\t344796\n", "NC_047559.1\t344861\t344863\n", "NC_047559.1\t433584\t433586\n", "NC_047559.1\t433588\t433590\n", "NC_047559.1\t433598\t433600\n", "NC_047559.1\t433645\t433647\n", "NC_047559.1\t618555\t618557\n", "NC_047559.1\t620221\t620223\n", "NC_047559.1\t632330\t632332\n", "NC_047559.1\t935578\t935580\n", "\n", "==> zr3644_22_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-downstreamFlanks <==\n", "NC_047559.1\t16061\t16063\n", "NC_047559.1\t16105\t16107\n", "NC_047559.1\t16112\t16114\n", "NC_047559.1\t16220\t16222\n", "NC_047559.1\t16260\t16262\n", "NC_047559.1\t16289\t16291\n", "NC_047559.1\t16310\t16312\n", "NC_047559.1\t16369\t16371\n", "NC_047559.1\t16409\t16411\n", "NC_047559.1\t16438\t16440\n", "\n", "==> zr3644_23_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-downstreamFlanks <==\n", "NC_047559.1\t433598\t433600\n", "NC_047559.1\t433645\t433647\n", "NC_047559.1\t576634\t576636\n", "NC_047559.1\t576693\t576695\n", "NC_047559.1\t576866\t576868\n", "NC_047559.1\t576880\t576882\n", "NC_047559.1\t577456\t577458\n", "NC_047559.1\t1190116\t1190118\n", "NC_047559.1\t1190165\t1190167\n", "NC_047559.1\t1190281\t1190283\n", "\n", "==> zr3644_23_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-downstreamFlanks <==\n", "NC_047559.1\t141853\t141855\n", "NC_047559.1\t141858\t141860\n", "NC_047559.1\t141868\t141870\n", "NC_047559.1\t141885\t141887\n", "NC_047559.1\t141888\t141890\n", "NC_047559.1\t141894\t141896\n", "NC_047559.1\t141905\t141907\n", "NC_047559.1\t142490\t142492\n", "NC_047559.1\t142504\t142506\n", "NC_047559.1\t142531\t142533\n", "\n", "==> zr3644_23_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-downstreamFlanks <==\n", "NC_047559.1\t16061\t16063\n", "NC_047559.1\t16105\t16107\n", "NC_047559.1\t16112\t16114\n", "NC_047559.1\t16220\t16222\n", "NC_047559.1\t16260\t16262\n", "NC_047559.1\t16289\t16291\n", "NC_047559.1\t16310\t16312\n", "NC_047559.1\t16369\t16371\n", "NC_047559.1\t16409\t16411\n", "NC_047559.1\t16438\t16440\n", "\n", "==> zr3644_24_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-downstreamFlanks <==\n", "NC_047559.1\t344623\t344625\n", "NC_047559.1\t433584\t433586\n", "NC_047559.1\t433588\t433590\n", "NC_047559.1\t433598\t433600\n", "NC_047559.1\t576634\t576636\n", "NC_047559.1\t576693\t576695\n", "NC_047559.1\t576752\t576754\n", "NC_047559.1\t576866\t576868\n", "NC_047559.1\t576880\t576882\n", "NC_047559.1\t1010136\t1010138\n", "\n", "==> zr3644_24_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-downstreamFlanks <==\n", "NC_047559.1\t142531\t142533\n", "NC_047559.1\t142593\t142595\n", "NC_047559.1\t264959\t264961\n", "NC_047559.1\t265013\t265015\n", "NC_047559.1\t265028\t265030\n", "NC_047559.1\t326197\t326199\n", "NC_047559.1\t344549\t344551\n", "NC_047559.1\t344785\t344787\n", "NC_047559.1\t344794\t344796\n", "NC_047559.1\t344812\t344814\n", "\n", "==> zr3644_24_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-downstreamFlanks <==\n", "NC_047559.1\t16061\t16063\n", "NC_047559.1\t16105\t16107\n", "NC_047559.1\t16112\t16114\n", "NC_047559.1\t16220\t16222\n", "NC_047559.1\t16260\t16262\n", "NC_047559.1\t16289\t16291\n", "NC_047559.1\t16310\t16312\n", "NC_047559.1\t16369\t16371\n", "NC_047559.1\t16409\t16411\n", "NC_047559.1\t16438\t16440\n", "\n", "==> zr3644_2_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-downstreamFlanks <==\n", "NC_047559.1\t433584\t433586\n", "NC_047559.1\t433588\t433590\n", "NC_047559.1\t433598\t433600\n", "NC_047559.1\t576634\t576636\n", "NC_047559.1\t576693\t576695\n", "NC_047559.1\t576866\t576868\n", "NC_047559.1\t576880\t576882\n", "NC_047559.1\t576914\t576916\n", "NC_047559.1\t577126\t577128\n", "NC_047559.1\t1010121\t1010123\n", "\n", "==> zr3644_2_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-downstreamFlanks <==\n", "NC_047559.1\t126668\t126670\n", "NC_047559.1\t142531\t142533\n", "NC_047559.1\t345009\t345011\n", "NC_047559.1\t433645\t433647\n", "NC_047559.1\t696340\t696342\n", "NC_047559.1\t696719\t696721\n", "NC_047559.1\t905877\t905879\n", "NC_047559.1\t956846\t956848\n", "NC_047559.1\t974957\t974959\n", "NC_047559.1\t1016510\t1016512\n", "\n", "==> zr3644_2_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-downstreamFlanks <==\n", "NC_047559.1\t12182\t12184\n", "NC_047559.1\t12229\t12231\n", "NC_047559.1\t12254\t12256\n", "NC_047559.1\t16061\t16063\n", "NC_047559.1\t16105\t16107\n", "NC_047559.1\t16112\t16114\n", "NC_047559.1\t16220\t16222\n", "NC_047559.1\t16260\t16262\n", "NC_047559.1\t16289\t16291\n", "NC_047559.1\t16310\t16312\n", "\n", "==> zr3644_3_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-downstreamFlanks <==\n", "NC_047559.1\t344549\t344551\n", "NC_047559.1\t433598\t433600\n", "NC_047559.1\t434252\t434254\n", "NC_047559.1\t576634\t576636\n", "NC_047559.1\t576693\t576695\n", "NC_047559.1\t576752\t576754\n", "NC_047559.1\t576866\t576868\n", "NC_047559.1\t576880\t576882\n", "NC_047559.1\t577126\t577128\n", "NC_047559.1\t577456\t577458\n", "\n", "==> zr3644_3_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-downstreamFlanks <==\n", "NC_047559.1\t265707\t265709\n", "NC_047559.1\t265710\t265712\n", "NC_047559.1\t433584\t433586\n", "NC_047559.1\t433588\t433590\n", "NC_047559.1\t434266\t434268\n", "NC_047559.1\t434308\t434310\n", "NC_047559.1\t576914\t576916\n", "NC_047559.1\t618577\t618579\n", "NC_047559.1\t618588\t618590\n", "NC_047559.1\t618592\t618594\n", "\n", "==> zr3644_3_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-downstreamFlanks <==\n", "NC_047559.1\t16061\t16063\n", "NC_047559.1\t16105\t16107\n", "NC_047559.1\t16112\t16114\n", "NC_047559.1\t16220\t16222\n", "NC_047559.1\t16260\t16262\n", "NC_047559.1\t16289\t16291\n", "NC_047559.1\t16310\t16312\n", "NC_047559.1\t16369\t16371\n", "NC_047559.1\t16409\t16411\n", "NC_047559.1\t16438\t16440\n", "\n", "==> zr3644_4_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-downstreamFlanks <==\n", "NC_047559.1\t344803\t344805\n", "NC_047559.1\t344829\t344831\n", "NC_047559.1\t344838\t344840\n", "NC_047559.1\t344861\t344863\n", "NC_047559.1\t433584\t433586\n", "NC_047559.1\t433588\t433590\n", "NC_047559.1\t433598\t433600\n", "NC_047559.1\t433645\t433647\n", "NC_047559.1\t576634\t576636\n", "NC_047559.1\t576693\t576695\n", "\n", "==> zr3644_4_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-downstreamFlanks <==\n", "NC_047559.1\t142531\t142533\n", "NC_047559.1\t142593\t142595\n", "NC_047559.1\t210041\t210043\n", "NC_047559.1\t264885\t264887\n", "NC_047559.1\t264911\t264913\n", "NC_047559.1\t264924\t264926\n", "NC_047559.1\t265013\t265015\n", "NC_047559.1\t265028\t265030\n", "NC_047559.1\t344549\t344551\n", "NC_047559.1\t344623\t344625\n", "\n", "==> zr3644_4_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-downstreamFlanks <==\n", "NC_047559.1\t16061\t16063\n", "NC_047559.1\t16105\t16107\n", "NC_047559.1\t16112\t16114\n", "NC_047559.1\t16220\t16222\n", "NC_047559.1\t16260\t16262\n", "NC_047559.1\t16289\t16291\n", "NC_047559.1\t16310\t16312\n", "NC_047559.1\t16369\t16371\n", "NC_047559.1\t16409\t16411\n", "NC_047559.1\t16438\t16440\n", "\n", "==> zr3644_5_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-downstreamFlanks <==\n", "NC_047559.1\t141853\t141855\n", "NC_047559.1\t141939\t141941\n", "NC_047559.1\t142371\t142373\n", "NC_047559.1\t142406\t142408\n", "NC_047559.1\t142411\t142413\n", "NC_047559.1\t142424\t142426\n", "NC_047559.1\t142447\t142449\n", "NC_047559.1\t142451\t142453\n", "NC_047559.1\t142484\t142486\n", "NC_047559.1\t142490\t142492\n", "\n", "==> zr3644_5_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-downstreamFlanks <==\n", "NC_047559.1\t141921\t141923\n", "NC_047559.1\t142531\t142533\n", "NC_047559.1\t344623\t344625\n", "NC_047559.1\t344803\t344805\n", "NC_047559.1\t344812\t344814\n", "NC_047559.1\t344829\t344831\n", "NC_047559.1\t344838\t344840\n", "NC_047559.1\t344861\t344863\n", "NC_047559.1\t433645\t433647\n", "NC_047559.1\t576914\t576916\n", "\n", "==> zr3644_5_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-downstreamFlanks <==\n", "NC_047559.1\t16061\t16063\n", "NC_047559.1\t16105\t16107\n", "NC_047559.1\t16112\t16114\n", "NC_047559.1\t16220\t16222\n", "NC_047559.1\t16260\t16262\n", "NC_047559.1\t16289\t16291\n", "NC_047559.1\t16310\t16312\n", "NC_047559.1\t16369\t16371\n", "NC_047559.1\t16409\t16411\n", "NC_047559.1\t16438\t16440\n", "\n", "==> zr3644_6_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-downstreamFlanks <==\n", "NC_047559.1\t142406\t142408\n", "NC_047559.1\t142411\t142413\n", "NC_047559.1\t142424\t142426\n", "NC_047559.1\t142447\t142449\n", "NC_047559.1\t142451\t142453\n", "NC_047559.1\t142465\t142467\n", "NC_047559.1\t142484\t142486\n", "NC_047559.1\t142490\t142492\n", "NC_047559.1\t142504\t142506\n", "NC_047559.1\t433598\t433600\n", "\n", "==> zr3644_6_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-downstreamFlanks <==\n", "NC_047559.1\t141853\t141855\n", "NC_047559.1\t141858\t141860\n", "NC_047559.1\t141868\t141870\n", "NC_047559.1\t141885\t141887\n", "NC_047559.1\t141888\t141890\n", "NC_047559.1\t141894\t141896\n", "NC_047559.1\t141905\t141907\n", "NC_047559.1\t141912\t141914\n", "NC_047559.1\t142531\t142533\n", "NC_047559.1\t142545\t142547\n", "\n", "==> zr3644_6_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-downstreamFlanks <==\n", "NC_047559.1\t12182\t12184\n", "NC_047559.1\t12229\t12231\n", "NC_047559.1\t12254\t12256\n", "NC_047559.1\t16061\t16063\n", "NC_047559.1\t16105\t16107\n", "NC_047559.1\t16112\t16114\n", "NC_047559.1\t16220\t16222\n", "NC_047559.1\t16260\t16262\n", "NC_047559.1\t16289\t16291\n", "NC_047559.1\t16310\t16312\n", "\n", "==> zr3644_7_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-downstreamFlanks <==\n", "NC_047559.1\t141868\t141870\n", "NC_047559.1\t141888\t141890\n", "NC_047559.1\t141905\t141907\n", "NC_047559.1\t142357\t142359\n", "NC_047559.1\t142371\t142373\n", "NC_047559.1\t142406\t142408\n", "NC_047559.1\t142411\t142413\n", "NC_047559.1\t142424\t142426\n", "NC_047559.1\t142465\t142467\n", "NC_047559.1\t142484\t142486\n", "\n", "==> zr3644_7_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-downstreamFlanks <==\n", "NC_047559.1\t141853\t141855\n", "NC_047559.1\t141858\t141860\n", "NC_047559.1\t141885\t141887\n", "NC_047559.1\t141894\t141896\n", "NC_047559.1\t142490\t142492\n", "NC_047559.1\t142504\t142506\n", "NC_047559.1\t142531\t142533\n", "NC_047559.1\t142545\t142547\n", "NC_047559.1\t142593\t142595\n", "NC_047559.1\t264885\t264887\n", "\n", "==> zr3644_7_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-downstreamFlanks <==\n", "NC_047559.1\t16061\t16063\n", "NC_047559.1\t16105\t16107\n", "NC_047559.1\t16112\t16114\n", "NC_047559.1\t16220\t16222\n", "NC_047559.1\t16260\t16262\n", "NC_047559.1\t16289\t16291\n", "NC_047559.1\t16310\t16312\n", "NC_047559.1\t16369\t16371\n", "NC_047559.1\t16409\t16411\n", "NC_047559.1\t16438\t16440\n", "\n", "==> zr3644_8_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-downstreamFlanks <==\n", "NC_047559.1\t344785\t344787\n", "NC_047559.1\t344794\t344796\n", "NC_047559.1\t344803\t344805\n", "NC_047559.1\t344812\t344814\n", "NC_047559.1\t344829\t344831\n", "NC_047559.1\t344838\t344840\n", "NC_047559.1\t576634\t576636\n", "NC_047559.1\t576693\t576695\n", "NC_047559.1\t576752\t576754\n", "NC_047559.1\t576866\t576868\n", "\n", "==> zr3644_8_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-downstreamFlanks <==\n", "NC_047559.1\t326072\t326074\n", "NC_047559.1\t326118\t326120\n", "NC_047559.1\t326295\t326297\n", "NC_047559.1\t326317\t326319\n", "NC_047559.1\t433598\t433600\n", "NC_047559.1\t468565\t468567\n", "NC_047559.1\t618610\t618612\n", "NC_047559.1\t956995\t956997\n", "NC_047559.1\t975058\t975060\n", "NC_047559.1\t1010303\t1010305\n", "\n", "==> zr3644_8_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-downstreamFlanks <==\n", "NC_047559.1\t12229\t12231\n", "NC_047559.1\t12254\t12256\n", "NC_047559.1\t16061\t16063\n", "NC_047559.1\t16105\t16107\n", "NC_047559.1\t16112\t16114\n", "NC_047559.1\t16220\t16222\n", "NC_047559.1\t16260\t16262\n", "NC_047559.1\t16289\t16291\n", "NC_047559.1\t16310\t16312\n", "NC_047559.1\t16369\t16371\n", "\n", "==> zr3644_9_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-downstreamFlanks <==\n", "NC_047559.1\t142406\t142408\n", "NC_047559.1\t142411\t142413\n", "NC_047559.1\t142424\t142426\n", "NC_047559.1\t142504\t142506\n", "NC_047559.1\t142531\t142533\n", "NC_047559.1\t142545\t142547\n", "NC_047559.1\t142593\t142595\n", "NC_047559.1\t344477\t344479\n", "NC_047559.1\t344549\t344551\n", "NC_047559.1\t344623\t344625\n", "\n", "==> zr3644_9_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-downstreamFlanks <==\n", "NC_047559.1\t325700\t325702\n", "NC_047559.1\t344812\t344814\n", "NC_047559.1\t344829\t344831\n", "NC_047559.1\t344838\t344840\n", "NC_047559.1\t344861\t344863\n", "NC_047559.1\t344972\t344974\n", "NC_047559.1\t344976\t344978\n", "NC_047559.1\t345009\t345011\n", "NC_047559.1\t345033\t345035\n", "NC_047559.1\t433645\t433647\n", "\n", "==> zr3644_9_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-downstreamFlanks <==\n", "NC_047559.1\t16061\t16063\n", "NC_047559.1\t16105\t16107\n", "NC_047559.1\t16112\t16114\n", "NC_047559.1\t16220\t16222\n", "NC_047559.1\t16260\t16262\n", "NC_047559.1\t16289\t16291\n", "NC_047559.1\t16310\t16312\n", "NC_047559.1\t16369\t16371\n", "NC_047559.1\t16409\t16411\n", "NC_047559.1\t16438\t16440\n", "\n", "==> zr3644_union-averages_5x.bedgraph-Meth.bed-downstreamFlanks <==\n", "NC_047559.1\t141853\t141855\n", "NC_047559.1\t141939\t141941\n", "NC_047559.1\t142406\t142408\n", "NC_047559.1\t142411\t142413\n", "NC_047559.1\t142424\t142426\n", "NC_047559.1\t142447\t142449\n", "NC_047559.1\t142451\t142453\n", "NC_047559.1\t433598\t433600\n", "NC_047559.1\t576634\t576636\n", "NC_047559.1\t576693\t576695\n", "\n", "==> zr3644_union-averages_5x.bedgraph-sparseMeth.bed-downstreamFlanks <==\n", "NC_047559.1\t141858\t141860\n", "NC_047559.1\t141868\t141870\n", "NC_047559.1\t141885\t141887\n", "NC_047559.1\t141888\t141890\n", "NC_047559.1\t141894\t141896\n", "NC_047559.1\t141905\t141907\n", "NC_047559.1\t141912\t141914\n", "NC_047559.1\t141921\t141923\n", "NC_047559.1\t142357\t142359\n", "NC_047559.1\t142371\t142373\n", "\n", "==> zr3644_union-averages_5x.bedgraph-unMeth.bed-downstreamFlanks <==\n", "NC_047559.1\t12182\t12184\n", "NC_047559.1\t12229\t12231\n", "NC_047559.1\t12254\t12256\n", "NC_047559.1\t16061\t16063\n", "NC_047559.1\t16105\t16107\n", "NC_047559.1\t16112\t16114\n", "NC_047559.1\t16220\t16222\n", "NC_047559.1\t16260\t16262\n", "NC_047559.1\t16289\t16291\n", "NC_047559.1\t16310\t16312\n" ] } ], "source": [ "#Check output\n", "!head *downstreamFlanks" ] }, { "cell_type": "code", "execution_count": 61, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ " 14259 zr3644_10_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-downstreamFlanks\n", " 22064 zr3644_10_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-downstreamFlanks\n", " 229754 zr3644_10_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-downstreamFlanks\n", " 15052 zr3644_11_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-downstreamFlanks\n", " 23547 zr3644_11_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-downstreamFlanks\n", " 244273 zr3644_11_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-downstreamFlanks\n", " 13711 zr3644_12_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-downstreamFlanks\n", " 20189 zr3644_12_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-downstreamFlanks\n", " 228132 zr3644_12_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-downstreamFlanks\n", " 14438 zr3644_13_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-downstreamFlanks\n", " 23164 zr3644_13_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-downstreamFlanks\n", " 239750 zr3644_13_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-downstreamFlanks\n", " 11430 zr3644_14_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-downstreamFlanks\n", " 15269 zr3644_14_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-downstreamFlanks\n", " 181022 zr3644_14_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-downstreamFlanks\n", " 16666 zr3644_15_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-downstreamFlanks\n", " 23954 zr3644_15_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-downstreamFlanks\n", " 252114 zr3644_15_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-downstreamFlanks\n", " 12848 zr3644_16_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-downstreamFlanks\n", " 20668 zr3644_16_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-downstreamFlanks\n", " 216192 zr3644_16_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-downstreamFlanks\n", " 14627 zr3644_17_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-downstreamFlanks\n", " 20104 zr3644_17_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-downstreamFlanks\n", " 236921 zr3644_17_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-downstreamFlanks\n", " 13381 zr3644_18_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-downstreamFlanks\n", " 21798 zr3644_18_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-downstreamFlanks\n", " 226630 zr3644_18_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-downstreamFlanks\n", " 12884 zr3644_19_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-downstreamFlanks\n", " 20667 zr3644_19_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-downstreamFlanks\n", " 223893 zr3644_19_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-downstreamFlanks\n", " 11910 zr3644_1_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-downstreamFlanks\n", " 20652 zr3644_1_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-downstreamFlanks\n", " 217244 zr3644_1_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-downstreamFlanks\n", " 13927 zr3644_20_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-downstreamFlanks\n", " 22119 zr3644_20_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-downstreamFlanks\n", " 237185 zr3644_20_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-downstreamFlanks\n", " 13861 zr3644_21_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-downstreamFlanks\n", " 22156 zr3644_21_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-downstreamFlanks\n", " 232654 zr3644_21_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-downstreamFlanks\n", " 12504 zr3644_22_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-downstreamFlanks\n", " 20303 zr3644_22_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-downstreamFlanks\n", " 214283 zr3644_22_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-downstreamFlanks\n", " 10665 zr3644_23_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-downstreamFlanks\n", " 17605 zr3644_23_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-downstreamFlanks\n", " 188380 zr3644_23_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-downstreamFlanks\n", " 13310 zr3644_24_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-downstreamFlanks\n", " 21202 zr3644_24_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-downstreamFlanks\n", " 232117 zr3644_24_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-downstreamFlanks\n", " 14982 zr3644_2_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-downstreamFlanks\n", " 19515 zr3644_2_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-downstreamFlanks\n", " 245061 zr3644_2_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-downstreamFlanks\n", " 10877 zr3644_3_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-downstreamFlanks\n", " 18405 zr3644_3_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-downstreamFlanks\n", " 191739 zr3644_3_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-downstreamFlanks\n", " 13349 zr3644_4_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-downstreamFlanks\n", " 21471 zr3644_4_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-downstreamFlanks\n", " 227181 zr3644_4_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-downstreamFlanks\n", " 12288 zr3644_5_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-downstreamFlanks\n", " 20115 zr3644_5_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-downstreamFlanks\n", " 210260 zr3644_5_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-downstreamFlanks\n", " 14033 zr3644_6_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-downstreamFlanks\n", " 22337 zr3644_6_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-downstreamFlanks\n", " 237127 zr3644_6_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-downstreamFlanks\n", " 18812 zr3644_7_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-downstreamFlanks\n", " 27865 zr3644_7_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-downstreamFlanks\n", " 297725 zr3644_7_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-downstreamFlanks\n", " 11985 zr3644_8_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-downstreamFlanks\n", " 19052 zr3644_8_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-downstreamFlanks\n", " 200007 zr3644_8_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-downstreamFlanks\n", " 11803 zr3644_9_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-downstreamFlanks\n", " 20289 zr3644_9_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-downstreamFlanks\n", " 202920 zr3644_9_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-downstreamFlanks\n", " 21839 zr3644_union-averages_5x.bedgraph-Meth.bed-downstreamFlanks\n", " 38167 zr3644_union-averages_5x.bedgraph-sparseMeth.bed-downstreamFlanks\n", " 390484 zr3644_union-averages_5x.bedgraph-unMeth.bed-downstreamFlanks\n", " 6691166 total\n" ] } ], "source": [ "#Count number of overlaps\n", "!wc -l *downstreamFlanks" ] }, { "cell_type": "code", "execution_count": 62, "metadata": { "collapsed": true }, "outputs": [], "source": [ "#Get line counts for each fine\n", "# Remove 28th line (total entries)\n", "#Ensure output is tab-delimited\n", "#Save output\n", "!wc -l *-downstreamFlanks \\\n", "| sed '76,$ d' \\\n", "| awk '{print $1\"\\t\"$2}' \\\n", "> zr3644_5x-downstreamFlanks-counts.txt" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "### 6h. Intergenic regions" ] }, { "cell_type": "code", "execution_count": 63, "metadata": { "collapsed": false }, "outputs": [], "source": [ "%%bash\n", "for f in *bed\n", "do\n", " /Users/Shared/bioinformatics/bedtools2/bin/intersectBed \\\n", " -u \\\n", " -a ${f} \\\n", " -b /Volumes/web-1/halfshell/genomic-databank/cgigas_uk_roslin_v1_intergenic.bed \\\n", " > ${f}-intergenic\n", "done" ] }, { "cell_type": "code", "execution_count": 64, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "==> zr3644_10_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-intergenic <==\n", "NC_047559.1\t4270\t4272\n", "NC_047559.1\t4791\t4793\n", "NC_047559.1\t4835\t4837\n", "NC_047559.1\t4843\t4845\n", "NC_047559.1\t4887\t4889\n", "NC_047559.1\t7490\t7492\n", "NC_047559.1\t7671\t7673\n", "NC_047559.1\t7814\t7816\n", "NC_047559.1\t7850\t7852\n", "NC_047559.1\t7867\t7869\n", "\n", "==> zr3644_10_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-intergenic <==\n", "NC_047559.1\t4397\t4399\n", "NC_047559.1\t4909\t4911\n", "NC_047559.1\t5500\t5502\n", "NC_047559.1\t7129\t7131\n", "NC_047559.1\t21982\t21984\n", "NC_047559.1\t23360\t23362\n", "NC_047559.1\t23610\t23612\n", "NC_047559.1\t25334\t25336\n", "NC_047559.1\t26448\t26450\n", "NC_047559.1\t26699\t26701\n", "\n", "==> zr3644_10_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-intergenic <==\n", "NC_047559.1\t20319\t20321\n", "NC_047559.1\t20341\t20343\n", "NC_047559.1\t20363\t20365\n", "NC_047559.1\t20385\t20387\n", "NC_047559.1\t20407\t20409\n", "NC_047559.1\t20429\t20431\n", "NC_047559.1\t20451\t20453\n", "NC_047559.1\t20924\t20926\n", "NC_047559.1\t20946\t20948\n", "NC_047559.1\t20954\t20956\n", "\n", "==> zr3644_11_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-intergenic <==\n", "NC_047559.1\t4843\t4845\n", "NC_047559.1\t4887\t4889\n", "NC_047559.1\t5316\t5318\n", "NC_047559.1\t7129\t7131\n", "NC_047559.1\t7490\t7492\n", "NC_047559.1\t7671\t7673\n", "NC_047559.1\t7814\t7816\n", "NC_047559.1\t7850\t7852\n", "NC_047559.1\t7867\t7869\n", "NC_047559.1\t7885\t7887\n", "\n", "==> zr3644_11_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-intergenic <==\n", "NC_047559.1\t4791\t4793\n", "NC_047559.1\t4835\t4837\n", "NC_047559.1\t4909\t4911\n", "NC_047559.1\t5605\t5607\n", "NC_047559.1\t5613\t5615\n", "NC_047559.1\t7716\t7718\n", "NC_047559.1\t8171\t8173\n", "NC_047559.1\t8449\t8451\n", "NC_047559.1\t8556\t8558\n", "NC_047559.1\t23610\t23612\n", "\n", "==> zr3644_11_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-intergenic <==\n", "NC_047559.1\t4397\t4399\n", "NC_047559.1\t5500\t5502\n", "NC_047559.1\t12503\t12505\n", "NC_047559.1\t12520\t12522\n", "NC_047559.1\t21834\t21836\n", "NC_047559.1\t21893\t21895\n", "NC_047559.1\t21938\t21940\n", "NC_047559.1\t21960\t21962\n", "NC_047559.1\t21982\t21984\n", "NC_047559.1\t22004\t22006\n", "\n", "==> zr3644_12_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-intergenic <==\n", "NC_047559.1\t4791\t4793\n", "NC_047559.1\t4835\t4837\n", "NC_047559.1\t4843\t4845\n", "NC_047559.1\t4887\t4889\n", "NC_047559.1\t7671\t7673\n", "NC_047559.1\t7814\t7816\n", "NC_047559.1\t7850\t7852\n", "NC_047559.1\t7867\t7869\n", "NC_047559.1\t7885\t7887\n", "NC_047559.1\t301219\t301221\n", "\n", "==> zr3644_12_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-intergenic <==\n", "NC_047559.1\t5500\t5502\n", "NC_047559.1\t7129\t7131\n", "NC_047559.1\t7490\t7492\n", "NC_047559.1\t8295\t8297\n", "NC_047559.1\t8308\t8310\n", "NC_047559.1\t8310\t8312\n", "NC_047559.1\t8346\t8348\n", "NC_047559.1\t8376\t8378\n", "NC_047559.1\t8414\t8416\n", "NC_047559.1\t22950\t22952\n", "\n", "==> zr3644_12_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-intergenic <==\n", "NC_047559.1\t5605\t5607\n", "NC_047559.1\t20946\t20948\n", "NC_047559.1\t20954\t20956\n", "NC_047559.1\t20960\t20962\n", "NC_047559.1\t20967\t20969\n", "NC_047559.1\t21798\t21800\n", "NC_047559.1\t21960\t21962\n", "NC_047559.1\t21982\t21984\n", "NC_047559.1\t22004\t22006\n", "NC_047559.1\t22026\t22028\n", "\n", "==> zr3644_13_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-intergenic <==\n", "NC_047559.1\t4791\t4793\n", "NC_047559.1\t4835\t4837\n", "NC_047559.1\t4843\t4845\n", "NC_047559.1\t4909\t4911\n", "NC_047559.1\t6486\t6488\n", "NC_047559.1\t6492\t6494\n", "NC_047559.1\t7129\t7131\n", "NC_047559.1\t7490\t7492\n", "NC_047559.1\t7671\t7673\n", "NC_047559.1\t7814\t7816\n", "\n", "==> zr3644_13_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-intergenic <==\n", "NC_047559.1\t4397\t4399\n", "NC_047559.1\t4887\t4889\n", "NC_047559.1\t5605\t5607\n", "NC_047559.1\t7716\t7718\n", "NC_047559.1\t8556\t8558\n", "NC_047559.1\t23360\t23362\n", "NC_047559.1\t23610\t23612\n", "NC_047559.1\t24926\t24928\n", "NC_047559.1\t24932\t24934\n", "NC_047559.1\t24934\t24936\n", "\n", "==> zr3644_13_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-intergenic <==\n", "NC_047559.1\t12503\t12505\n", "NC_047559.1\t12520\t12522\n", "NC_047559.1\t12992\t12994\n", "NC_047559.1\t13061\t13063\n", "NC_047559.1\t20297\t20299\n", "NC_047559.1\t20319\t20321\n", "NC_047559.1\t20341\t20343\n", "NC_047559.1\t20363\t20365\n", "NC_047559.1\t20385\t20387\n", "NC_047559.1\t20407\t20409\n", "\n", "==> zr3644_14_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-intergenic <==\n", "NC_047559.1\t4791\t4793\n", "NC_047559.1\t4835\t4837\n", "NC_047559.1\t4843\t4845\n", "NC_047559.1\t24926\t24928\n", "NC_047559.1\t24932\t24934\n", "NC_047559.1\t24934\t24936\n", "NC_047559.1\t299369\t299371\n", "NC_047559.1\t301247\t301249\n", "NC_047559.1\t301400\t301402\n", "NC_047559.1\t1011758\t1011760\n", "\n", "==> zr3644_14_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-intergenic <==\n", "NC_047559.1\t5605\t5607\n", "NC_047559.1\t5613\t5615\n", "NC_047559.1\t23360\t23362\n", "NC_047559.1\t23610\t23612\n", "NC_047559.1\t31135\t31137\n", "NC_047559.1\t33595\t33597\n", "NC_047559.1\t41242\t41244\n", "NC_047559.1\t50492\t50494\n", "NC_047559.1\t56037\t56039\n", "NC_047559.1\t56073\t56075\n", "\n", "==> zr3644_14_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-intergenic <==\n", "NC_047559.1\t12906\t12908\n", "NC_047559.1\t12923\t12925\n", "NC_047559.1\t12992\t12994\n", "NC_047559.1\t13061\t13063\n", "NC_047559.1\t20319\t20321\n", "NC_047559.1\t20341\t20343\n", "NC_047559.1\t20363\t20365\n", "NC_047559.1\t20385\t20387\n", "NC_047559.1\t20407\t20409\n", "NC_047559.1\t21938\t21940\n", "\n", "==> zr3644_15_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-intergenic <==\n", "NC_047559.1\t4791\t4793\n", "NC_047559.1\t4835\t4837\n", "NC_047559.1\t4843\t4845\n", "NC_047559.1\t4887\t4889\n", "NC_047559.1\t4909\t4911\n", "NC_047559.1\t5316\t5318\n", "NC_047559.1\t5605\t5607\n", "NC_047559.1\t5613\t5615\n", "NC_047559.1\t7129\t7131\n", "NC_047559.1\t7490\t7492\n", "\n", "==> zr3644_15_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-intergenic <==\n", "NC_047559.1\t2809\t2811\n", "NC_047559.1\t4397\t4399\n", "NC_047559.1\t5500\t5502\n", "NC_047559.1\t5999\t6001\n", "NC_047559.1\t20297\t20299\n", "NC_047559.1\t20946\t20948\n", "NC_047559.1\t23610\t23612\n", "NC_047559.1\t24066\t24068\n", "NC_047559.1\t24751\t24753\n", "NC_047559.1\t26746\t26748\n", "\n", "==> zr3644_15_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-intergenic <==\n", "NC_047559.1\t7716\t7718\n", "NC_047559.1\t20252\t20254\n", "NC_047559.1\t20319\t20321\n", "NC_047559.1\t20341\t20343\n", "NC_047559.1\t20363\t20365\n", "NC_047559.1\t20385\t20387\n", "NC_047559.1\t20407\t20409\n", "NC_047559.1\t20429\t20431\n", "NC_047559.1\t20451\t20453\n", "NC_047559.1\t20924\t20926\n", "\n", "==> zr3644_16_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-intergenic <==\n", "NC_047559.1\t4791\t4793\n", "NC_047559.1\t4835\t4837\n", "NC_047559.1\t4843\t4845\n", "NC_047559.1\t4887\t4889\n", "NC_047559.1\t4909\t4911\n", "NC_047559.1\t7129\t7131\n", "NC_047559.1\t7490\t7492\n", "NC_047559.1\t7671\t7673\n", "NC_047559.1\t7814\t7816\n", "NC_047559.1\t7850\t7852\n", "\n", "==> zr3644_16_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-intergenic <==\n", "NC_047559.1\t20363\t20365\n", "NC_047559.1\t23610\t23612\n", "NC_047559.1\t24251\t24253\n", "NC_047559.1\t25334\t25336\n", "NC_047559.1\t37587\t37589\n", "NC_047559.1\t45248\t45250\n", "NC_047559.1\t45698\t45700\n", "NC_047559.1\t46678\t46680\n", "NC_047559.1\t56037\t56039\n", "NC_047559.1\t56073\t56075\n", "\n", "==> zr3644_16_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-intergenic <==\n", "NC_047559.1\t7716\t7718\n", "NC_047559.1\t20319\t20321\n", "NC_047559.1\t20341\t20343\n", "NC_047559.1\t20385\t20387\n", "NC_047559.1\t20407\t20409\n", "NC_047559.1\t20429\t20431\n", "NC_047559.1\t20451\t20453\n", "NC_047559.1\t21834\t21836\n", "NC_047559.1\t21893\t21895\n", "NC_047559.1\t21938\t21940\n", "\n", "==> zr3644_17_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-intergenic <==\n", "NC_047559.1\t4791\t4793\n", "NC_047559.1\t4835\t4837\n", "NC_047559.1\t4843\t4845\n", "NC_047559.1\t4887\t4889\n", "NC_047559.1\t5613\t5615\n", "NC_047559.1\t7490\t7492\n", "NC_047559.1\t24066\t24068\n", "NC_047559.1\t44918\t44920\n", "NC_047559.1\t147333\t147335\n", "NC_047559.1\t147335\t147337\n", "\n", "==> zr3644_17_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-intergenic <==\n", "NC_047559.1\t4073\t4075\n", "NC_047559.1\t4909\t4911\n", "NC_047559.1\t5316\t5318\n", "NC_047559.1\t5500\t5502\n", "NC_047559.1\t5605\t5607\n", "NC_047559.1\t7129\t7131\n", "NC_047559.1\t20193\t20195\n", "NC_047559.1\t21834\t21836\n", "NC_047559.1\t22070\t22072\n", "NC_047559.1\t22092\t22094\n", "\n", "==> zr3644_17_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-intergenic <==\n", "NC_047559.1\t5883\t5885\n", "NC_047559.1\t12503\t12505\n", "NC_047559.1\t12520\t12522\n", "NC_047559.1\t12554\t12556\n", "NC_047559.1\t13061\t13063\n", "NC_047559.1\t20252\t20254\n", "NC_047559.1\t20297\t20299\n", "NC_047559.1\t20588\t20590\n", "NC_047559.1\t21798\t21800\n", "NC_047559.1\t21893\t21895\n", "\n", "==> zr3644_18_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-intergenic <==\n", "NC_047559.1\t4835\t4837\n", "NC_047559.1\t4843\t4845\n", "NC_047559.1\t4909\t4911\n", "NC_047559.1\t5500\t5502\n", "NC_047559.1\t7129\t7131\n", "NC_047559.1\t7490\t7492\n", "NC_047559.1\t7671\t7673\n", "NC_047559.1\t7850\t7852\n", "NC_047559.1\t7867\t7869\n", "NC_047559.1\t7885\t7887\n", "\n", "==> zr3644_18_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-intergenic <==\n", "NC_047559.1\t4791\t4793\n", "NC_047559.1\t4887\t4889\n", "NC_047559.1\t5316\t5318\n", "NC_047559.1\t5605\t5607\n", "NC_047559.1\t5613\t5615\n", "NC_047559.1\t7716\t7718\n", "NC_047559.1\t8346\t8348\n", "NC_047559.1\t8376\t8378\n", "NC_047559.1\t8414\t8416\n", "NC_047559.1\t8449\t8451\n", "\n", "==> zr3644_18_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-intergenic <==\n", "NC_047559.1\t4397\t4399\n", "NC_047559.1\t13061\t13063\n", "NC_047559.1\t21893\t21895\n", "NC_047559.1\t21938\t21940\n", "NC_047559.1\t21960\t21962\n", "NC_047559.1\t21982\t21984\n", "NC_047559.1\t22004\t22006\n", "NC_047559.1\t22026\t22028\n", "NC_047559.1\t22442\t22444\n", "NC_047559.1\t22565\t22567\n", "\n", "==> zr3644_19_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-intergenic <==\n", "NC_047559.1\t4835\t4837\n", "NC_047559.1\t4843\t4845\n", "NC_047559.1\t4887\t4889\n", "NC_047559.1\t4909\t4911\n", "NC_047559.1\t7129\t7131\n", "NC_047559.1\t7490\t7492\n", "NC_047559.1\t7671\t7673\n", "NC_047559.1\t7814\t7816\n", "NC_047559.1\t7850\t7852\n", "NC_047559.1\t7867\t7869\n", "\n", "==> zr3644_19_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-intergenic <==\n", "NC_047559.1\t4791\t4793\n", "NC_047559.1\t8346\t8348\n", "NC_047559.1\t8449\t8451\n", "NC_047559.1\t22026\t22028\n", "NC_047559.1\t22070\t22072\n", "NC_047559.1\t23360\t23362\n", "NC_047559.1\t23610\t23612\n", "NC_047559.1\t26083\t26085\n", "NC_047559.1\t32640\t32642\n", "NC_047559.1\t33210\t33212\n", "\n", "==> zr3644_19_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-intergenic <==\n", "NC_047559.1\t12503\t12505\n", "NC_047559.1\t12520\t12522\n", "NC_047559.1\t13061\t13063\n", "NC_047559.1\t20341\t20343\n", "NC_047559.1\t20363\t20365\n", "NC_047559.1\t20946\t20948\n", "NC_047559.1\t20954\t20956\n", "NC_047559.1\t20960\t20962\n", "NC_047559.1\t20967\t20969\n", "NC_047559.1\t21834\t21836\n", "\n", "==> zr3644_1_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-intergenic <==\n", "NC_047559.1\t2267\t2269\n", "NC_047559.1\t2291\t2293\n", "NC_047559.1\t4791\t4793\n", "NC_047559.1\t4835\t4837\n", "NC_047559.1\t4843\t4845\n", "NC_047559.1\t7129\t7131\n", "NC_047559.1\t7490\t7492\n", "NC_047559.1\t7885\t7887\n", "NC_047559.1\t7923\t7925\n", "NC_047559.1\t7939\t7941\n", "\n", "==> zr3644_1_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-intergenic <==\n", "NC_047559.1\t4887\t4889\n", "NC_047559.1\t23360\t23362\n", "NC_047559.1\t23610\t23612\n", "NC_047559.1\t26509\t26511\n", "NC_047559.1\t26561\t26563\n", "NC_047559.1\t26591\t26593\n", "NC_047559.1\t36850\t36852\n", "NC_047559.1\t39537\t39539\n", "NC_047559.1\t41242\t41244\n", "NC_047559.1\t42392\t42394\n", "\n", "==> zr3644_1_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-intergenic <==\n", "NC_047559.1\t20363\t20365\n", "NC_047559.1\t20385\t20387\n", "NC_047559.1\t20407\t20409\n", "NC_047559.1\t20429\t20431\n", "NC_047559.1\t21960\t21962\n", "NC_047559.1\t21982\t21984\n", "NC_047559.1\t22004\t22006\n", "NC_047559.1\t22026\t22028\n", "NC_047559.1\t22048\t22050\n", "NC_047559.1\t22070\t22072\n", "\n", "==> zr3644_20_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-intergenic <==\n", "NC_047559.1\t4397\t4399\n", "NC_047559.1\t4843\t4845\n", "NC_047559.1\t5605\t5607\n", "NC_047559.1\t7129\t7131\n", "NC_047559.1\t7490\t7492\n", "NC_047559.1\t7671\t7673\n", "NC_047559.1\t7814\t7816\n", "NC_047559.1\t7850\t7852\n", "NC_047559.1\t7867\t7869\n", "NC_047559.1\t7885\t7887\n", "\n", "==> zr3644_20_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-intergenic <==\n", "NC_047559.1\t4791\t4793\n", "NC_047559.1\t4835\t4837\n", "NC_047559.1\t4887\t4889\n", "NC_047559.1\t4909\t4911\n", "NC_047559.1\t5613\t5615\n", "NC_047559.1\t7716\t7718\n", "NC_047559.1\t8251\t8253\n", "NC_047559.1\t8266\t8268\n", "NC_047559.1\t8346\t8348\n", "NC_047559.1\t8376\t8378\n", "\n", "==> zr3644_20_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-intergenic <==\n", "NC_047559.1\t20252\t20254\n", "NC_047559.1\t20297\t20299\n", "NC_047559.1\t20319\t20321\n", "NC_047559.1\t20341\t20343\n", "NC_047559.1\t20363\t20365\n", "NC_047559.1\t20385\t20387\n", "NC_047559.1\t20407\t20409\n", "NC_047559.1\t20429\t20431\n", "NC_047559.1\t20924\t20926\n", "NC_047559.1\t20938\t20940\n", "\n", "==> zr3644_21_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-intergenic <==\n", "NC_047559.1\t4791\t4793\n", "NC_047559.1\t4835\t4837\n", "NC_047559.1\t4843\t4845\n", "NC_047559.1\t4887\t4889\n", "NC_047559.1\t4909\t4911\n", "NC_047559.1\t7129\t7131\n", "NC_047559.1\t7490\t7492\n", "NC_047559.1\t7671\t7673\n", "NC_047559.1\t7814\t7816\n", "NC_047559.1\t7850\t7852\n", "\n", "==> zr3644_21_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-intergenic <==\n", "NC_047559.1\t4397\t4399\n", "NC_047559.1\t7716\t7718\n", "NC_047559.1\t7979\t7981\n", "NC_047559.1\t7990\t7992\n", "NC_047559.1\t8236\t8238\n", "NC_047559.1\t8251\t8253\n", "NC_047559.1\t8254\t8256\n", "NC_047559.1\t8346\t8348\n", "NC_047559.1\t23610\t23612\n", "NC_047559.1\t23952\t23954\n", "\n", "==> zr3644_21_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-intergenic <==\n", "NC_047559.1\t21798\t21800\n", "NC_047559.1\t21834\t21836\n", "NC_047559.1\t21893\t21895\n", "NC_047559.1\t21938\t21940\n", "NC_047559.1\t21960\t21962\n", "NC_047559.1\t21982\t21984\n", "NC_047559.1\t22004\t22006\n", "NC_047559.1\t22026\t22028\n", "NC_047559.1\t22048\t22050\n", "NC_047559.1\t22070\t22072\n", "\n", "==> zr3644_22_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-intergenic <==\n", "NC_047559.1\t4791\t4793\n", "NC_047559.1\t4835\t4837\n", "NC_047559.1\t4843\t4845\n", "NC_047559.1\t4887\t4889\n", "NC_047559.1\t4909\t4911\n", "NC_047559.1\t5605\t5607\n", "NC_047559.1\t7129\t7131\n", "NC_047559.1\t7490\t7492\n", "NC_047559.1\t7671\t7673\n", "NC_047559.1\t7814\t7816\n", "\n", "==> zr3644_22_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-intergenic <==\n", "NC_047559.1\t5500\t5502\n", "NC_047559.1\t5613\t5615\n", "NC_047559.1\t21729\t21731\n", "NC_047559.1\t25334\t25336\n", "NC_047559.1\t26463\t26465\n", "NC_047559.1\t42762\t42764\n", "NC_047559.1\t42791\t42793\n", "NC_047559.1\t46845\t46847\n", "NC_047559.1\t49031\t49033\n", "NC_047559.1\t51178\t51180\n", "\n", "==> zr3644_22_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-intergenic <==\n", "NC_047559.1\t20252\t20254\n", "NC_047559.1\t20297\t20299\n", "NC_047559.1\t20319\t20321\n", "NC_047559.1\t20341\t20343\n", "NC_047559.1\t20363\t20365\n", "NC_047559.1\t20385\t20387\n", "NC_047559.1\t20407\t20409\n", "NC_047559.1\t20429\t20431\n", "NC_047559.1\t20451\t20453\n", "NC_047559.1\t21798\t21800\n", "\n", "==> zr3644_23_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-intergenic <==\n", "NC_047559.1\t4835\t4837\n", "NC_047559.1\t4843\t4845\n", "NC_047559.1\t4887\t4889\n", "NC_047559.1\t7129\t7131\n", "NC_047559.1\t7490\t7492\n", "NC_047559.1\t7671\t7673\n", "NC_047559.1\t7814\t7816\n", "NC_047559.1\t7850\t7852\n", "NC_047559.1\t7867\t7869\n", "NC_047559.1\t7885\t7887\n", "\n", "==> zr3644_23_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-intergenic <==\n", "NC_047559.1\t4791\t4793\n", "NC_047559.1\t4909\t4911\n", "NC_047559.1\t5605\t5607\n", "NC_047559.1\t8346\t8348\n", "NC_047559.1\t23610\t23612\n", "NC_047559.1\t24926\t24928\n", "NC_047559.1\t25334\t25336\n", "NC_047559.1\t36160\t36162\n", "NC_047559.1\t42415\t42417\n", "NC_047559.1\t44210\t44212\n", "\n", "==> zr3644_23_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-intergenic <==\n", "NC_047559.1\t20924\t20926\n", "NC_047559.1\t20946\t20948\n", "NC_047559.1\t20954\t20956\n", "NC_047559.1\t20960\t20962\n", "NC_047559.1\t20967\t20969\n", "NC_047559.1\t21798\t21800\n", "NC_047559.1\t21834\t21836\n", "NC_047559.1\t21893\t21895\n", "NC_047559.1\t21938\t21940\n", "NC_047559.1\t21960\t21962\n", "\n", "==> zr3644_24_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-intergenic <==\n", "NC_047559.1\t1571\t1573\n", "NC_047559.1\t4835\t4837\n", "NC_047559.1\t4843\t4845\n", "NC_047559.1\t4887\t4889\n", "NC_047559.1\t4909\t4911\n", "NC_047559.1\t7129\t7131\n", "NC_047559.1\t7490\t7492\n", "NC_047559.1\t7671\t7673\n", "NC_047559.1\t7814\t7816\n", "NC_047559.1\t7850\t7852\n", "\n", "==> zr3644_24_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-intergenic <==\n", "NC_047559.1\t4791\t4793\n", "NC_047559.1\t7716\t7718\n", "NC_047559.1\t8346\t8348\n", "NC_047559.1\t8556\t8558\n", "NC_047559.1\t22579\t22581\n", "NC_047559.1\t23610\t23612\n", "NC_047559.1\t25334\t25336\n", "NC_047559.1\t26699\t26701\n", "NC_047559.1\t26738\t26740\n", "NC_047559.1\t27132\t27134\n", "\n", "==> zr3644_24_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-intergenic <==\n", "NC_047559.1\t12992\t12994\n", "NC_047559.1\t13061\t13063\n", "NC_047559.1\t20924\t20926\n", "NC_047559.1\t20938\t20940\n", "NC_047559.1\t20946\t20948\n", "NC_047559.1\t20954\t20956\n", "NC_047559.1\t20960\t20962\n", "NC_047559.1\t20967\t20969\n", "NC_047559.1\t21798\t21800\n", "NC_047559.1\t21834\t21836\n", "\n", "==> zr3644_2_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-intergenic <==\n", "NC_047559.1\t4073\t4075\n", "NC_047559.1\t4791\t4793\n", "NC_047559.1\t4835\t4837\n", "NC_047559.1\t4843\t4845\n", "NC_047559.1\t4887\t4889\n", "NC_047559.1\t4909\t4911\n", "NC_047559.1\t5500\t5502\n", "NC_047559.1\t7129\t7131\n", "NC_047559.1\t7490\t7492\n", "NC_047559.1\t7671\t7673\n", "\n", "==> zr3644_2_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-intergenic <==\n", "NC_047559.1\t5291\t5293\n", "NC_047559.1\t5605\t5607\n", "NC_047559.1\t5613\t5615\n", "NC_047559.1\t7716\t7718\n", "NC_047559.1\t7959\t7961\n", "NC_047559.1\t7979\t7981\n", "NC_047559.1\t7990\t7992\n", "NC_047559.1\t22587\t22589\n", "NC_047559.1\t22601\t22603\n", "NC_047559.1\t27880\t27882\n", "\n", "==> zr3644_2_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-intergenic <==\n", "NC_047559.1\t5316\t5318\n", "NC_047559.1\t12439\t12441\n", "NC_047559.1\t12503\t12505\n", "NC_047559.1\t12520\t12522\n", "NC_047559.1\t20341\t20343\n", "NC_047559.1\t20363\t20365\n", "NC_047559.1\t20385\t20387\n", "NC_047559.1\t20407\t20409\n", "NC_047559.1\t20429\t20431\n", "NC_047559.1\t21960\t21962\n", "\n", "==> zr3644_3_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-intergenic <==\n", "NC_047559.1\t4791\t4793\n", "NC_047559.1\t4835\t4837\n", "NC_047559.1\t4843\t4845\n", "NC_047559.1\t4887\t4889\n", "NC_047559.1\t7129\t7131\n", "NC_047559.1\t7490\t7492\n", "NC_047559.1\t7671\t7673\n", "NC_047559.1\t7716\t7718\n", "NC_047559.1\t7814\t7816\n", "NC_047559.1\t7867\t7869\n", "\n", "==> zr3644_3_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-intergenic <==\n", "NC_047559.1\t8266\t8268\n", "NC_047559.1\t8295\t8297\n", "NC_047559.1\t8346\t8348\n", "NC_047559.1\t8376\t8378\n", "NC_047559.1\t23610\t23612\n", "NC_047559.1\t24926\t24928\n", "NC_047559.1\t24932\t24934\n", "NC_047559.1\t24934\t24936\n", "NC_047559.1\t26955\t26957\n", "NC_047559.1\t38030\t38032\n", "\n", "==> zr3644_3_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-intergenic <==\n", "NC_047559.1\t4909\t4911\n", "NC_047559.1\t8251\t8253\n", "NC_047559.1\t8254\t8256\n", "NC_047559.1\t20385\t20387\n", "NC_047559.1\t20407\t20409\n", "NC_047559.1\t20451\t20453\n", "NC_047559.1\t21938\t21940\n", "NC_047559.1\t21960\t21962\n", "NC_047559.1\t21982\t21984\n", "NC_047559.1\t22004\t22006\n", "\n", "==> zr3644_4_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-intergenic <==\n", "NC_047559.1\t4073\t4075\n", "NC_047559.1\t4270\t4272\n", "NC_047559.1\t4887\t4889\n", "NC_047559.1\t4909\t4911\n", "NC_047559.1\t7129\t7131\n", "NC_047559.1\t7490\t7492\n", "NC_047559.1\t7671\t7673\n", "NC_047559.1\t7814\t7816\n", "NC_047559.1\t7850\t7852\n", "NC_047559.1\t7867\t7869\n", "\n", "==> zr3644_4_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-intergenic <==\n", "NC_047559.1\t4791\t4793\n", "NC_047559.1\t4835\t4837\n", "NC_047559.1\t4843\t4845\n", "NC_047559.1\t5500\t5502\n", "NC_047559.1\t5605\t5607\n", "NC_047559.1\t5613\t5615\n", "NC_047559.1\t24926\t24928\n", "NC_047559.1\t26419\t26421\n", "NC_047559.1\t26448\t26450\n", "NC_047559.1\t26463\t26465\n", "\n", "==> zr3644_4_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-intergenic <==\n", "NC_047559.1\t4397\t4399\n", "NC_047559.1\t12906\t12908\n", "NC_047559.1\t20252\t20254\n", "NC_047559.1\t20297\t20299\n", "NC_047559.1\t21590\t21592\n", "NC_047559.1\t21611\t21613\n", "NC_047559.1\t21798\t21800\n", "NC_047559.1\t21834\t21836\n", "NC_047559.1\t21893\t21895\n", "NC_047559.1\t21938\t21940\n", "\n", "==> zr3644_5_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-intergenic <==\n", "NC_047559.1\t4791\t4793\n", "NC_047559.1\t4835\t4837\n", "NC_047559.1\t4843\t4845\n", "NC_047559.1\t4887\t4889\n", "NC_047559.1\t4909\t4911\n", "NC_047559.1\t7129\t7131\n", "NC_047559.1\t7490\t7492\n", "NC_047559.1\t7671\t7673\n", "NC_047559.1\t7814\t7816\n", "NC_047559.1\t7850\t7852\n", "\n", "==> zr3644_5_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-intergenic <==\n", "NC_047559.1\t4270\t4272\n", "NC_047559.1\t4397\t4399\n", "NC_047559.1\t5605\t5607\n", "NC_047559.1\t5613\t5615\n", "NC_047559.1\t7716\t7718\n", "NC_047559.1\t8556\t8558\n", "NC_047559.1\t23610\t23612\n", "NC_047559.1\t25334\t25336\n", "NC_047559.1\t26419\t26421\n", "NC_047559.1\t26463\t26465\n", "\n", "==> zr3644_5_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-intergenic <==\n", "NC_047559.1\t20363\t20365\n", "NC_047559.1\t20385\t20387\n", "NC_047559.1\t20407\t20409\n", "NC_047559.1\t20429\t20431\n", "NC_047559.1\t21938\t21940\n", "NC_047559.1\t21960\t21962\n", "NC_047559.1\t21982\t21984\n", "NC_047559.1\t22442\t22444\n", "NC_047559.1\t22565\t22567\n", "NC_047559.1\t22579\t22581\n", "\n", "==> zr3644_6_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-intergenic <==\n", "NC_047559.1\t2087\t2089\n", "NC_047559.1\t4835\t4837\n", "NC_047559.1\t4843\t4845\n", "NC_047559.1\t4887\t4889\n", "NC_047559.1\t4909\t4911\n", "NC_047559.1\t7129\t7131\n", "NC_047559.1\t7814\t7816\n", "NC_047559.1\t7850\t7852\n", "NC_047559.1\t7867\t7869\n", "NC_047559.1\t7885\t7887\n", "\n", "==> zr3644_6_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-intergenic <==\n", "NC_047559.1\t4791\t4793\n", "NC_047559.1\t5500\t5502\n", "NC_047559.1\t7490\t7492\n", "NC_047559.1\t7671\t7673\n", "NC_047559.1\t8236\t8238\n", "NC_047559.1\t23610\t23612\n", "NC_047559.1\t25334\t25336\n", "NC_047559.1\t27132\t27134\n", "NC_047559.1\t30373\t30375\n", "NC_047559.1\t30382\t30384\n", "\n", "==> zr3644_6_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-intergenic <==\n", "NC_047559.1\t4397\t4399\n", "NC_047559.1\t5883\t5885\n", "NC_047559.1\t6528\t6530\n", "NC_047559.1\t7716\t7718\n", "NC_047559.1\t12503\t12505\n", "NC_047559.1\t12520\t12522\n", "NC_047559.1\t12554\t12556\n", "NC_047559.1\t12992\t12994\n", "NC_047559.1\t13061\t13063\n", "NC_047559.1\t20319\t20321\n", "\n", "==> zr3644_7_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-intergenic <==\n", "NC_047559.1\t4270\t4272\n", "NC_047559.1\t4835\t4837\n", "NC_047559.1\t4887\t4889\n", "NC_047559.1\t5605\t5607\n", "NC_047559.1\t5613\t5615\n", "NC_047559.1\t7129\t7131\n", "NC_047559.1\t7490\t7492\n", "NC_047559.1\t7671\t7673\n", "NC_047559.1\t7814\t7816\n", "NC_047559.1\t7850\t7852\n", "\n", "==> zr3644_7_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-intergenic <==\n", "NC_047559.1\t1571\t1573\n", "NC_047559.1\t4397\t4399\n", "NC_047559.1\t4791\t4793\n", "NC_047559.1\t4843\t4845\n", "NC_047559.1\t4909\t4911\n", "NC_047559.1\t5291\t5293\n", "NC_047559.1\t5316\t5318\n", "NC_047559.1\t5500\t5502\n", "NC_047559.1\t5883\t5885\n", "NC_047559.1\t6439\t6441\n", "\n", "==> zr3644_7_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-intergenic <==\n", "NC_047559.1\t20319\t20321\n", "NC_047559.1\t20341\t20343\n", "NC_047559.1\t20363\t20365\n", "NC_047559.1\t20385\t20387\n", "NC_047559.1\t20407\t20409\n", "NC_047559.1\t20429\t20431\n", "NC_047559.1\t20451\t20453\n", "NC_047559.1\t20473\t20475\n", "NC_047559.1\t21893\t21895\n", "NC_047559.1\t21938\t21940\n", "\n", "==> zr3644_8_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-intergenic <==\n", "NC_047559.1\t4397\t4399\n", "NC_047559.1\t4835\t4837\n", "NC_047559.1\t4843\t4845\n", "NC_047559.1\t4887\t4889\n", "NC_047559.1\t4909\t4911\n", "NC_047559.1\t5605\t5607\n", "NC_047559.1\t5613\t5615\n", "NC_047559.1\t7129\t7131\n", "NC_047559.1\t7490\t7492\n", "NC_047559.1\t7671\t7673\n", "\n", "==> zr3644_8_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-intergenic <==\n", "NC_047559.1\t4791\t4793\n", "NC_047559.1\t7716\t7718\n", "NC_047559.1\t8171\t8173\n", "NC_047559.1\t8217\t8219\n", "NC_047559.1\t8254\t8256\n", "NC_047559.1\t8346\t8348\n", "NC_047559.1\t8376\t8378\n", "NC_047559.1\t8414\t8416\n", "NC_047559.1\t23610\t23612\n", "NC_047559.1\t26699\t26701\n", "\n", "==> zr3644_8_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-intergenic <==\n", "NC_047559.1\t12503\t12505\n", "NC_047559.1\t12520\t12522\n", "NC_047559.1\t12992\t12994\n", "NC_047559.1\t13061\t13063\n", "NC_047559.1\t20319\t20321\n", "NC_047559.1\t20363\t20365\n", "NC_047559.1\t20385\t20387\n", "NC_047559.1\t20407\t20409\n", "NC_047559.1\t21893\t21895\n", "NC_047559.1\t21938\t21940\n", "\n", "==> zr3644_9_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-intergenic <==\n", "NC_047559.1\t4073\t4075\n", "NC_047559.1\t4791\t4793\n", "NC_047559.1\t4835\t4837\n", "NC_047559.1\t4843\t4845\n", "NC_047559.1\t4887\t4889\n", "NC_047559.1\t5605\t5607\n", "NC_047559.1\t5613\t5615\n", "NC_047559.1\t7129\t7131\n", "NC_047559.1\t7490\t7492\n", "NC_047559.1\t7814\t7816\n", "\n", "==> zr3644_9_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-intergenic <==\n", "NC_047559.1\t7716\t7718\n", "NC_047559.1\t23610\t23612\n", "NC_047559.1\t24091\t24093\n", "NC_047559.1\t25334\t25336\n", "NC_047559.1\t25858\t25860\n", "NC_047559.1\t35403\t35405\n", "NC_047559.1\t35473\t35475\n", "NC_047559.1\t42709\t42711\n", "NC_047559.1\t45010\t45012\n", "NC_047559.1\t45033\t45035\n", "\n", "==> zr3644_9_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-intergenic <==\n", "NC_047559.1\t20252\t20254\n", "NC_047559.1\t20297\t20299\n", "NC_047559.1\t20319\t20321\n", "NC_047559.1\t20341\t20343\n", "NC_047559.1\t20363\t20365\n", "NC_047559.1\t20385\t20387\n", "NC_047559.1\t20407\t20409\n", "NC_047559.1\t20429\t20431\n", "NC_047559.1\t21834\t21836\n", "NC_047559.1\t21893\t21895\n", "\n", "==> zr3644_union-averages_5x.bedgraph-Meth.bed-intergenic <==\n", "NC_047559.1\t1571\t1573\n", "NC_047559.1\t2087\t2089\n", "NC_047559.1\t2267\t2269\n", "NC_047559.1\t2291\t2293\n", "NC_047559.1\t4073\t4075\n", "NC_047559.1\t4791\t4793\n", "NC_047559.1\t4835\t4837\n", "NC_047559.1\t4843\t4845\n", "NC_047559.1\t4887\t4889\n", "NC_047559.1\t4909\t4911\n", "\n", "==> zr3644_union-averages_5x.bedgraph-sparseMeth.bed-intergenic <==\n", "NC_047559.1\t2809\t2811\n", "NC_047559.1\t4270\t4272\n", "NC_047559.1\t4397\t4399\n", "NC_047559.1\t5291\t5293\n", "NC_047559.1\t5316\t5318\n", "NC_047559.1\t5500\t5502\n", "NC_047559.1\t5605\t5607\n", "NC_047559.1\t5613\t5615\n", "NC_047559.1\t5999\t6001\n", "NC_047559.1\t6439\t6441\n", "\n", "==> zr3644_union-averages_5x.bedgraph-unMeth.bed-intergenic <==\n", "NC_047559.1\t5883\t5885\n", "NC_047559.1\t6528\t6530\n", "NC_047559.1\t12439\t12441\n", "NC_047559.1\t12503\t12505\n", "NC_047559.1\t12520\t12522\n", "NC_047559.1\t12554\t12556\n", "NC_047559.1\t12906\t12908\n", "NC_047559.1\t12923\t12925\n", "NC_047559.1\t12992\t12994\n", "NC_047559.1\t13061\t13063\n" ] } ], "source": [ "#Check output\n", "!head *intergenic" ] }, { "cell_type": "code", "execution_count": 65, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ " 22733 zr3644_10_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-intergenic\n", " 119886 zr3644_10_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-intergenic\n", " 1748992 zr3644_10_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-intergenic\n", " 23815 zr3644_11_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-intergenic\n", " 126168 zr3644_11_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-intergenic\n", " 1860431 zr3644_11_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-intergenic\n", " 18892 zr3644_12_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-intergenic\n", " 107574 zr3644_12_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-intergenic\n", " 1694738 zr3644_12_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-intergenic\n", " 22700 zr3644_13_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-intergenic\n", " 123761 zr3644_13_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-intergenic\n", " 1824195 zr3644_13_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-intergenic\n", " 21245 zr3644_14_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-intergenic\n", " 85600 zr3644_14_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-intergenic\n", " 1354817 zr3644_14_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-intergenic\n", " 26098 zr3644_15_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-intergenic\n", " 129047 zr3644_15_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-intergenic\n", " 1922758 zr3644_15_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-intergenic\n", " 20663 zr3644_16_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-intergenic\n", " 110884 zr3644_16_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-intergenic\n", " 1644032 zr3644_16_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-intergenic\n", " 25922 zr3644_17_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-intergenic\n", " 110541 zr3644_17_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-intergenic\n", " 1818838 zr3644_17_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-intergenic\n", " 20616 zr3644_18_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-intergenic\n", " 115449 zr3644_18_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-intergenic\n", " 1704671 zr3644_18_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-intergenic\n", " 19936 zr3644_19_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-intergenic\n", " 109959 zr3644_19_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-intergenic\n", " 1707201 zr3644_19_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-intergenic\n", " 18567 zr3644_1_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-intergenic\n", " 102884 zr3644_1_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-intergenic\n", " 1659044 zr3644_1_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-intergenic\n", " 21387 zr3644_20_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-intergenic\n", " 120500 zr3644_20_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-intergenic\n", " 1802973 zr3644_20_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-intergenic\n", " 21475 zr3644_21_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-intergenic\n", " 118254 zr3644_21_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-intergenic\n", " 1762882 zr3644_21_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-intergenic\n", " 19636 zr3644_22_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-intergenic\n", " 108556 zr3644_22_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-intergenic\n", " 1634165 zr3644_22_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-intergenic\n", " 16385 zr3644_23_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-intergenic\n", " 96125 zr3644_23_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-intergenic\n", " 1435513 zr3644_23_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-intergenic\n", " 21621 zr3644_24_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-intergenic\n", " 114168 zr3644_24_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-intergenic\n", " 1758292 zr3644_24_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-intergenic\n", " 25722 zr3644_2_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-intergenic\n", " 109418 zr3644_2_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-intergenic\n", " 1852727 zr3644_2_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-intergenic\n", " 17748 zr3644_3_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-intergenic\n", " 99522 zr3644_3_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-intergenic\n", " 1459211 zr3644_3_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-intergenic\n", " 19789 zr3644_4_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-intergenic\n", " 112907 zr3644_4_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-intergenic\n", " 1742132 zr3644_4_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-intergenic\n", " 19177 zr3644_5_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-intergenic\n", " 107252 zr3644_5_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-intergenic\n", " 1597914 zr3644_5_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-intergenic\n", " 21664 zr3644_6_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-intergenic\n", " 119033 zr3644_6_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-intergenic\n", " 1793379 zr3644_6_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-intergenic\n", " 29690 zr3644_7_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-intergenic\n", " 151620 zr3644_7_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-intergenic\n", " 2309920 zr3644_7_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-intergenic\n", " 19336 zr3644_8_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-intergenic\n", " 104505 zr3644_8_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-intergenic\n", " 1528777 zr3644_8_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-intergenic\n", " 19982 zr3644_9_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-intergenic\n", " 111204 zr3644_9_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-intergenic\n", " 1558738 zr3644_9_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-intergenic\n", " 32028 zr3644_union-averages_5x.bedgraph-Meth.bed-intergenic\n", " 180062 zr3644_union-averages_5x.bedgraph-sparseMeth.bed-intergenic\n", " 3272003 zr3644_union-averages_5x.bedgraph-unMeth.bed-intergenic\n", " 47890049 total\n" ] } ], "source": [ "#Count number of overlaps\n", "!wc -l *intergenic" ] }, { "cell_type": "code", "execution_count": 66, "metadata": { "collapsed": true }, "outputs": [], "source": [ "#Get line counts for each fine\n", "# Remove 28th line (total entries)\n", "#Ensure output is tab-delimited\n", "#Save output\n", "!wc -l *-intergenic \\\n", "| sed '76,$ d' \\\n", "| awk '{print $1\"\\t\"$2}' \\\n", "> zr3644_5x-intergenic-counts.txt" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "### 6i. lncRNA" ] }, { "cell_type": "code", "execution_count": 67, "metadata": { "collapsed": false }, "outputs": [], "source": [ "%%bash\n", "for f in *bed\n", "do\n", " /Users/Shared/bioinformatics/bedtools2/bin/intersectBed \\\n", " -u \\\n", " -a ${f} \\\n", " -b /Volumes/web-1/halfshell/genomic-databank/cgigas_uk_roslin_v1_lncRNA.gff \\\n", " > ${f}-lncRNA\n", "done" ] }, { "cell_type": "code", "execution_count": 68, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "==> zr3644_10_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-lncRNA <==\n", "NC_047559.1\t416078\t416080\n", "NC_047559.1\t416920\t416922\n", "NC_047559.1\t418539\t418541\n", "NC_047559.1\t418551\t418553\n", "NC_047559.1\t418582\t418584\n", "NC_047559.1\t418592\t418594\n", "NC_047559.1\t1664745\t1664747\n", "NC_047559.1\t1664773\t1664775\n", "NC_047559.1\t1688433\t1688435\n", "NC_047559.1\t1688466\t1688468\n", "\n", "==> zr3644_10_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-lncRNA <==\n", "NC_047559.1\t10270\t10272\n", "NC_047559.1\t10292\t10294\n", "NC_047559.1\t10358\t10360\n", "NC_047559.1\t242614\t242616\n", "NC_047559.1\t258015\t258017\n", "NC_047559.1\t416052\t416054\n", "NC_047559.1\t416071\t416073\n", "NC_047559.1\t416088\t416090\n", "NC_047559.1\t419514\t419516\n", "NC_047559.1\t419784\t419786\n", "\n", "==> zr3644_10_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-lncRNA <==\n", "NC_047559.1\t10314\t10316\n", "NC_047559.1\t10845\t10847\n", "NC_047559.1\t10859\t10861\n", "NC_047559.1\t10899\t10901\n", "NC_047559.1\t10920\t10922\n", "NC_047559.1\t10950\t10952\n", "NC_047559.1\t11000\t11002\n", "NC_047559.1\t11026\t11028\n", "NC_047559.1\t226734\t226736\n", "NC_047559.1\t226739\t226741\n", "\n", "==> zr3644_11_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-lncRNA <==\n", "NC_047559.1\t419514\t419516\n", "NC_047559.1\t419587\t419589\n", "NC_047559.1\t419606\t419608\n", "NC_047559.1\t1664745\t1664747\n", "NC_047559.1\t3828724\t3828726\n", "NC_047559.1\t3828793\t3828795\n", "NC_047559.1\t3829511\t3829513\n", "NC_047559.1\t3829591\t3829593\n", "NC_047559.1\t3829807\t3829809\n", "NC_047559.1\t3829827\t3829829\n", "\n", "==> zr3644_11_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-lncRNA <==\n", "NC_047559.1\t419473\t419475\n", "NC_047559.1\t419784\t419786\n", "NC_047559.1\t786896\t786898\n", "NC_047559.1\t788943\t788945\n", "NC_047559.1\t788951\t788953\n", "NC_047559.1\t788970\t788972\n", "NC_047559.1\t1213634\t1213636\n", "NC_047559.1\t1213643\t1213645\n", "NC_047559.1\t1213726\t1213728\n", "NC_047559.1\t1213731\t1213733\n", "\n", "==> zr3644_11_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-lncRNA <==\n", "NC_047559.1\t10155\t10157\n", "NC_047559.1\t10215\t10217\n", "NC_047559.1\t10270\t10272\n", "NC_047559.1\t10292\t10294\n", "NC_047559.1\t10314\t10316\n", "NC_047559.1\t10358\t10360\n", "NC_047559.1\t10402\t10404\n", "NC_047559.1\t10413\t10415\n", "NC_047559.1\t10457\t10459\n", "NC_047559.1\t10479\t10481\n", "\n", "==> zr3644_12_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-lncRNA <==\n", "NC_047559.1\t3828724\t3828726\n", "NC_047559.1\t3828793\t3828795\n", "NC_047559.1\t3828838\t3828840\n", "NC_047559.1\t3829511\t3829513\n", "NC_047559.1\t3829591\t3829593\n", "NC_047559.1\t3830168\t3830170\n", "NC_047559.1\t3830230\t3830232\n", "NC_047559.1\t3830275\t3830277\n", "NC_047559.1\t4377912\t4377914\n", "NC_047559.1\t4400440\t4400442\n", "\n", "==> zr3644_12_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-lncRNA <==\n", "NC_047559.1\t10358\t10360\n", "NC_047559.1\t10772\t10774\n", "NC_047559.1\t416920\t416922\n", "NC_047559.1\t419514\t419516\n", "NC_047559.1\t789704\t789706\n", "NC_047559.1\t789744\t789746\n", "NC_047559.1\t789774\t789776\n", "NC_047559.1\t2133589\t2133591\n", "NC_047559.1\t2133616\t2133618\n", "NC_047559.1\t2133633\t2133635\n", "\n", "==> zr3644_12_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-lncRNA <==\n", "NC_047559.1\t10215\t10217\n", "NC_047559.1\t10270\t10272\n", "NC_047559.1\t10292\t10294\n", "NC_047559.1\t10314\t10316\n", "NC_047559.1\t10402\t10404\n", "NC_047559.1\t10413\t10415\n", "NC_047559.1\t10457\t10459\n", "NC_047559.1\t10479\t10481\n", "NC_047559.1\t10501\t10503\n", "NC_047559.1\t10545\t10547\n", "\n", "==> zr3644_13_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-lncRNA <==\n", "NC_047559.1\t416088\t416090\n", "NC_047559.1\t416920\t416922\n", "NC_047559.1\t417944\t417946\n", "NC_047559.1\t418551\t418553\n", "NC_047559.1\t418569\t418571\n", "NC_047559.1\t418582\t418584\n", "NC_047559.1\t418592\t418594\n", "NC_047559.1\t3828724\t3828726\n", "NC_047559.1\t3828793\t3828795\n", "NC_047559.1\t3829511\t3829513\n", "\n", "==> zr3644_13_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-lncRNA <==\n", "NC_047559.1\t10270\t10272\n", "NC_047559.1\t415957\t415959\n", "NC_047559.1\t415975\t415977\n", "NC_047559.1\t415988\t415990\n", "NC_047559.1\t415998\t416000\n", "NC_047559.1\t416052\t416054\n", "NC_047559.1\t416071\t416073\n", "NC_047559.1\t418447\t418449\n", "NC_047559.1\t418539\t418541\n", "NC_047559.1\t419514\t419516\n", "\n", "==> zr3644_13_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-lncRNA <==\n", "NC_047559.1\t10292\t10294\n", "NC_047559.1\t10314\t10316\n", "NC_047559.1\t10358\t10360\n", "NC_047559.1\t10479\t10481\n", "NC_047559.1\t10501\t10503\n", "NC_047559.1\t10545\t10547\n", "NC_047559.1\t10547\t10549\n", "NC_047559.1\t10567\t10569\n", "NC_047559.1\t10772\t10774\n", "NC_047559.1\t10845\t10847\n", "\n", "==> zr3644_14_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-lncRNA <==\n", "NC_047559.1\t416920\t416922\n", "NC_047559.1\t417944\t417946\n", "NC_047559.1\t418038\t418040\n", "NC_047559.1\t419514\t419516\n", "NC_047559.1\t1664745\t1664747\n", "NC_047559.1\t1664773\t1664775\n", "NC_047559.1\t1664902\t1664904\n", "NC_047559.1\t3828724\t3828726\n", "NC_047559.1\t3828793\t3828795\n", "NC_047559.1\t3828838\t3828840\n", "\n", "==> zr3644_14_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-lncRNA <==\n", "NC_047559.1\t10457\t10459\n", "NC_047559.1\t2133510\t2133512\n", "NC_047559.1\t2133663\t2133665\n", "NC_047559.1\t2133845\t2133847\n", "NC_047559.1\t2136045\t2136047\n", "NC_047559.1\t2200837\t2200839\n", "NC_047559.1\t2201220\t2201222\n", "NC_047559.1\t2910787\t2910789\n", "NC_047559.1\t3026701\t3026703\n", "NC_047559.1\t3027522\t3027524\n", "\n", "==> zr3644_14_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-lncRNA <==\n", "NC_047559.1\t10270\t10272\n", "NC_047559.1\t10292\t10294\n", "NC_047559.1\t10314\t10316\n", "NC_047559.1\t10358\t10360\n", "NC_047559.1\t10391\t10393\n", "NC_047559.1\t10402\t10404\n", "NC_047559.1\t10413\t10415\n", "NC_047559.1\t10479\t10481\n", "NC_047559.1\t10545\t10547\n", "NC_047559.1\t10612\t10614\n", "\n", "==> zr3644_15_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-lncRNA <==\n", "NC_047559.1\t1213634\t1213636\n", "NC_047559.1\t1213643\t1213645\n", "NC_047559.1\t1213726\t1213728\n", "NC_047559.1\t1213731\t1213733\n", "NC_047559.1\t1664745\t1664747\n", "NC_047559.1\t1664773\t1664775\n", "NC_047559.1\t1664902\t1664904\n", "NC_047559.1\t2198255\t2198257\n", "NC_047559.1\t3828724\t3828726\n", "NC_047559.1\t3828793\t3828795\n", "\n", "==> zr3644_15_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-lncRNA <==\n", "NC_047559.1\t10215\t10217\n", "NC_047559.1\t228525\t228527\n", "NC_047559.1\t788914\t788916\n", "NC_047559.1\t788918\t788920\n", "NC_047559.1\t788943\t788945\n", "NC_047559.1\t788951\t788953\n", "NC_047559.1\t788970\t788972\n", "NC_047559.1\t1213812\t1213814\n", "NC_047559.1\t2198406\t2198408\n", "NC_047559.1\t2200764\t2200766\n", "\n", "==> zr3644_15_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-lncRNA <==\n", "NC_047559.1\t10155\t10157\n", "NC_047559.1\t10270\t10272\n", "NC_047559.1\t10292\t10294\n", "NC_047559.1\t10314\t10316\n", "NC_047559.1\t10358\t10360\n", "NC_047559.1\t10391\t10393\n", "NC_047559.1\t10457\t10459\n", "NC_047559.1\t10479\t10481\n", "NC_047559.1\t10501\t10503\n", "NC_047559.1\t10545\t10547\n", "\n", "==> zr3644_16_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-lncRNA <==\n", "NC_047559.1\t419606\t419608\n", "NC_047559.1\t419784\t419786\n", "NC_047559.1\t3828724\t3828726\n", "NC_047559.1\t3829511\t3829513\n", "NC_047559.1\t3829591\t3829593\n", "NC_047559.1\t3829807\t3829809\n", "NC_047559.1\t3829827\t3829829\n", "NC_047559.1\t3829837\t3829839\n", "NC_047559.1\t3829843\t3829845\n", "NC_047559.1\t3829865\t3829867\n", "\n", "==> zr3644_16_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-lncRNA <==\n", "NC_047559.1\t416920\t416922\n", "NC_047559.1\t419473\t419475\n", "NC_047559.1\t419514\t419516\n", "NC_047559.1\t419587\t419589\n", "NC_047559.1\t786722\t786724\n", "NC_047559.1\t1213643\t1213645\n", "NC_047559.1\t1213726\t1213728\n", "NC_047559.1\t1213731\t1213733\n", "NC_047559.1\t1248156\t1248158\n", "NC_047559.1\t1248160\t1248162\n", "\n", "==> zr3644_16_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-lncRNA <==\n", "NC_047559.1\t10845\t10847\n", "NC_047559.1\t10859\t10861\n", "NC_047559.1\t10899\t10901\n", "NC_047559.1\t10920\t10922\n", "NC_047559.1\t10950\t10952\n", "NC_047559.1\t226734\t226736\n", "NC_047559.1\t226739\t226741\n", "NC_047559.1\t226793\t226795\n", "NC_047559.1\t226835\t226837\n", "NC_047559.1\t226850\t226852\n", "\n", "==> zr3644_17_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-lncRNA <==\n", "NC_047559.1\t416920\t416922\n", "NC_047559.1\t419514\t419516\n", "NC_047559.1\t1664745\t1664747\n", "NC_047559.1\t1664773\t1664775\n", "NC_047559.1\t1665259\t1665261\n", "NC_047559.1\t1687707\t1687709\n", "NC_047559.1\t2133633\t2133635\n", "NC_047559.1\t2133663\t2133665\n", "NC_047559.1\t3828724\t3828726\n", "NC_047559.1\t3829511\t3829513\n", "\n", "==> zr3644_17_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-lncRNA <==\n", "NC_047559.1\t228335\t228337\n", "NC_047559.1\t418038\t418040\n", "NC_047559.1\t1247606\t1247608\n", "NC_047559.1\t1247627\t1247629\n", "NC_047559.1\t1247837\t1247839\n", "NC_047559.1\t1688423\t1688425\n", "NC_047559.1\t1688433\t1688435\n", "NC_047559.1\t1688466\t1688468\n", "NC_047559.1\t1689118\t1689120\n", "NC_047559.1\t2133510\t2133512\n", "\n", "==> zr3644_17_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-lncRNA <==\n", "NC_047559.1\t10380\t10382\n", "NC_047559.1\t10391\t10393\n", "NC_047559.1\t10402\t10404\n", "NC_047559.1\t10413\t10415\n", "NC_047559.1\t10457\t10459\n", "NC_047559.1\t10479\t10481\n", "NC_047559.1\t10501\t10503\n", "NC_047559.1\t10545\t10547\n", "NC_047559.1\t10547\t10549\n", "NC_047559.1\t10567\t10569\n", "\n", "==> zr3644_18_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-lncRNA <==\n", "NC_047559.1\t416920\t416922\n", "NC_047559.1\t418672\t418674\n", "NC_047559.1\t1664745\t1664747\n", "NC_047559.1\t1664773\t1664775\n", "NC_047559.1\t1664902\t1664904\n", "NC_047559.1\t3828724\t3828726\n", "NC_047559.1\t3828793\t3828795\n", "NC_047559.1\t3829511\t3829513\n", "NC_047559.1\t3829591\t3829593\n", "NC_047559.1\t3829807\t3829809\n", "\n", "==> zr3644_18_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-lncRNA <==\n", "NC_047559.1\t10358\t10360\n", "NC_047559.1\t11026\t11028\n", "NC_047559.1\t242920\t242922\n", "NC_047559.1\t415714\t415716\n", "NC_047559.1\t415739\t415741\n", "NC_047559.1\t415822\t415824\n", "NC_047559.1\t415957\t415959\n", "NC_047559.1\t415975\t415977\n", "NC_047559.1\t415988\t415990\n", "NC_047559.1\t415998\t416000\n", "\n", "==> zr3644_18_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-lncRNA <==\n", "NC_047559.1\t10270\t10272\n", "NC_047559.1\t10292\t10294\n", "NC_047559.1\t10314\t10316\n", "NC_047559.1\t10380\t10382\n", "NC_047559.1\t10391\t10393\n", "NC_047559.1\t10402\t10404\n", "NC_047559.1\t10413\t10415\n", "NC_047559.1\t10457\t10459\n", "NC_047559.1\t10479\t10481\n", "NC_047559.1\t10501\t10503\n", "\n", "==> zr3644_19_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-lncRNA <==\n", "NC_047559.1\t416757\t416759\n", "NC_047559.1\t419606\t419608\n", "NC_047559.1\t1213634\t1213636\n", "NC_047559.1\t1213643\t1213645\n", "NC_047559.1\t1664745\t1664747\n", "NC_047559.1\t1664773\t1664775\n", "NC_047559.1\t1688423\t1688425\n", "NC_047559.1\t1688433\t1688435\n", "NC_047559.1\t1688466\t1688468\n", "NC_047559.1\t3828724\t3828726\n", "\n", "==> zr3644_19_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-lncRNA <==\n", "NC_047559.1\t11080\t11082\n", "NC_047559.1\t242485\t242487\n", "NC_047559.1\t255789\t255791\n", "NC_047559.1\t416920\t416922\n", "NC_047559.1\t419514\t419516\n", "NC_047559.1\t419587\t419589\n", "NC_047559.1\t419784\t419786\n", "NC_047559.1\t788426\t788428\n", "NC_047559.1\t789341\t789343\n", "NC_047559.1\t1213726\t1213728\n", "\n", "==> zr3644_19_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-lncRNA <==\n", "NC_047559.1\t10155\t10157\n", "NC_047559.1\t10215\t10217\n", "NC_047559.1\t10270\t10272\n", "NC_047559.1\t10292\t10294\n", "NC_047559.1\t10314\t10316\n", "NC_047559.1\t10358\t10360\n", "NC_047559.1\t10402\t10404\n", "NC_047559.1\t10413\t10415\n", "NC_047559.1\t10457\t10459\n", "NC_047559.1\t10479\t10481\n", "\n", "==> zr3644_1_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-lncRNA <==\n", "NC_047559.1\t420980\t420982\n", "NC_047559.1\t421032\t421034\n", "NC_047559.1\t1664658\t1664660\n", "NC_047559.1\t1664745\t1664747\n", "NC_047559.1\t1664773\t1664775\n", "NC_047559.1\t1665101\t1665103\n", "NC_047559.1\t1665111\t1665113\n", "NC_047559.1\t1665148\t1665150\n", "NC_047559.1\t1665259\t1665261\n", "NC_047559.1\t2133510\t2133512\n", "\n", "==> zr3644_1_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-lncRNA <==\n", "NC_047559.1\t416920\t416922\n", "NC_047559.1\t419514\t419516\n", "NC_047559.1\t419784\t419786\n", "NC_047559.1\t419933\t419935\n", "NC_047559.1\t785575\t785577\n", "NC_047559.1\t1664708\t1664710\n", "NC_047559.1\t1664902\t1664904\n", "NC_047559.1\t1690247\t1690249\n", "NC_047559.1\t2133579\t2133581\n", "NC_047559.1\t2133589\t2133591\n", "\n", "==> zr3644_1_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-lncRNA <==\n", "NC_047559.1\t10215\t10217\n", "NC_047559.1\t10270\t10272\n", "NC_047559.1\t10292\t10294\n", "NC_047559.1\t10314\t10316\n", "NC_047559.1\t10358\t10360\n", "NC_047559.1\t10380\t10382\n", "NC_047559.1\t10391\t10393\n", "NC_047559.1\t10402\t10404\n", "NC_047559.1\t10413\t10415\n", "NC_047559.1\t10457\t10459\n", "\n", "==> zr3644_20_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-lncRNA <==\n", "NC_047559.1\t416920\t416922\n", "NC_047559.1\t1214656\t1214658\n", "NC_047559.1\t1215016\t1215018\n", "NC_047559.1\t1664658\t1664660\n", "NC_047559.1\t1664745\t1664747\n", "NC_047559.1\t1664773\t1664775\n", "NC_047559.1\t1664902\t1664904\n", "NC_047559.1\t1665259\t1665261\n", "NC_047559.1\t2133510\t2133512\n", "NC_047559.1\t2133579\t2133581\n", "\n", "==> zr3644_20_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-lncRNA <==\n", "NC_047559.1\t419514\t419516\n", "NC_047559.1\t1213726\t1213728\n", "NC_047559.1\t1213731\t1213733\n", "NC_047559.1\t1213812\t1213814\n", "NC_047559.1\t1214079\t1214081\n", "NC_047559.1\t1248363\t1248365\n", "NC_047559.1\t1248757\t1248759\n", "NC_047559.1\t1248759\t1248761\n", "NC_047559.1\t1248911\t1248913\n", "NC_047559.1\t1248921\t1248923\n", "\n", "==> zr3644_20_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-lncRNA <==\n", "NC_047559.1\t10270\t10272\n", "NC_047559.1\t10292\t10294\n", "NC_047559.1\t10314\t10316\n", "NC_047559.1\t10358\t10360\n", "NC_047559.1\t10402\t10404\n", "NC_047559.1\t10413\t10415\n", "NC_047559.1\t10479\t10481\n", "NC_047559.1\t10501\t10503\n", "NC_047559.1\t10545\t10547\n", "NC_047559.1\t10547\t10549\n", "\n", "==> zr3644_21_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-lncRNA <==\n", "NC_047559.1\t419514\t419516\n", "NC_047559.1\t1664587\t1664589\n", "NC_047559.1\t1664745\t1664747\n", "NC_047559.1\t1664773\t1664775\n", "NC_047559.1\t3828724\t3828726\n", "NC_047559.1\t3828793\t3828795\n", "NC_047559.1\t3829511\t3829513\n", "NC_047559.1\t3829591\t3829593\n", "NC_047559.1\t3829807\t3829809\n", "NC_047559.1\t3829827\t3829829\n", "\n", "==> zr3644_21_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-lncRNA <==\n", "NC_047559.1\t227856\t227858\n", "NC_047559.1\t418447\t418449\n", "NC_047559.1\t419473\t419475\n", "NC_047559.1\t419784\t419786\n", "NC_047559.1\t1213634\t1213636\n", "NC_047559.1\t1213643\t1213645\n", "NC_047559.1\t1213726\t1213728\n", "NC_047559.1\t1213731\t1213733\n", "NC_047559.1\t1213812\t1213814\n", "NC_047559.1\t1664457\t1664459\n", "\n", "==> zr3644_21_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-lncRNA <==\n", "NC_047559.1\t10155\t10157\n", "NC_047559.1\t10215\t10217\n", "NC_047559.1\t10270\t10272\n", "NC_047559.1\t10292\t10294\n", "NC_047559.1\t10314\t10316\n", "NC_047559.1\t10479\t10481\n", "NC_047559.1\t10501\t10503\n", "NC_047559.1\t10545\t10547\n", "NC_047559.1\t10547\t10549\n", "NC_047559.1\t10645\t10647\n", "\n", "==> zr3644_22_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-lncRNA <==\n", "NC_047559.1\t419606\t419608\n", "NC_047559.1\t419784\t419786\n", "NC_047559.1\t1664457\t1664459\n", "NC_047559.1\t1664745\t1664747\n", "NC_047559.1\t1664773\t1664775\n", "NC_047559.1\t3828724\t3828726\n", "NC_047559.1\t3829511\t3829513\n", "NC_047559.1\t3829591\t3829593\n", "NC_047559.1\t3829807\t3829809\n", "NC_047559.1\t3829827\t3829829\n", "\n", "==> zr3644_22_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-lncRNA <==\n", "NC_047559.1\t11080\t11082\n", "NC_047559.1\t419514\t419516\n", "NC_047559.1\t419587\t419589\n", "NC_047559.1\t1213634\t1213636\n", "NC_047559.1\t1213643\t1213645\n", "NC_047559.1\t1213726\t1213728\n", "NC_047559.1\t1213731\t1213733\n", "NC_047559.1\t1213812\t1213814\n", "NC_047559.1\t1248160\t1248162\n", "NC_047559.1\t1248704\t1248706\n", "\n", "==> zr3644_22_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-lncRNA <==\n", "NC_047559.1\t10155\t10157\n", "NC_047559.1\t10270\t10272\n", "NC_047559.1\t10292\t10294\n", "NC_047559.1\t10314\t10316\n", "NC_047559.1\t10457\t10459\n", "NC_047559.1\t10479\t10481\n", "NC_047559.1\t10501\t10503\n", "NC_047559.1\t10545\t10547\n", "NC_047559.1\t10547\t10549\n", "NC_047559.1\t10567\t10569\n", "\n", "==> zr3644_23_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-lncRNA <==\n", "NC_047559.1\t1664745\t1664747\n", "NC_047559.1\t1664773\t1664775\n", "NC_047559.1\t1664902\t1664904\n", "NC_047559.1\t3828724\t3828726\n", "NC_047559.1\t3828793\t3828795\n", "NC_047559.1\t3829511\t3829513\n", "NC_047559.1\t3829591\t3829593\n", "NC_047559.1\t3829807\t3829809\n", "NC_047559.1\t3829827\t3829829\n", "NC_047559.1\t3829837\t3829839\n", "\n", "==> zr3644_23_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-lncRNA <==\n", "NC_047559.1\t416920\t416922\n", "NC_047559.1\t419514\t419516\n", "NC_047559.1\t419606\t419608\n", "NC_047559.1\t789510\t789512\n", "NC_047559.1\t1249426\t1249428\n", "NC_047559.1\t2133510\t2133512\n", "NC_047559.1\t2133589\t2133591\n", "NC_047559.1\t2133616\t2133618\n", "NC_047559.1\t2133633\t2133635\n", "NC_047559.1\t2133663\t2133665\n", "\n", "==> zr3644_23_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-lncRNA <==\n", "NC_047559.1\t10270\t10272\n", "NC_047559.1\t10292\t10294\n", "NC_047559.1\t10314\t10316\n", "NC_047559.1\t10358\t10360\n", "NC_047559.1\t10545\t10547\n", "NC_047559.1\t10547\t10549\n", "NC_047559.1\t10567\t10569\n", "NC_047559.1\t10592\t10594\n", "NC_047559.1\t10772\t10774\n", "NC_047559.1\t10845\t10847\n", "\n", "==> zr3644_24_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-lncRNA <==\n", "NC_047559.1\t419514\t419516\n", "NC_047559.1\t419784\t419786\n", "NC_047559.1\t1664457\t1664459\n", "NC_047559.1\t1664459\t1664461\n", "NC_047559.1\t1664773\t1664775\n", "NC_047559.1\t1688466\t1688468\n", "NC_047559.1\t2133510\t2133512\n", "NC_047559.1\t2911584\t2911586\n", "NC_047559.1\t3828724\t3828726\n", "NC_047559.1\t3829511\t3829513\n", "\n", "==> zr3644_24_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-lncRNA <==\n", "NC_047559.1\t10547\t10549\n", "NC_047559.1\t10645\t10647\n", "NC_047559.1\t10950\t10952\n", "NC_047559.1\t416078\t416080\n", "NC_047559.1\t417944\t417946\n", "NC_047559.1\t419933\t419935\n", "NC_047559.1\t786013\t786015\n", "NC_047559.1\t1248722\t1248724\n", "NC_047559.1\t1248757\t1248759\n", "NC_047559.1\t1248759\t1248761\n", "\n", "==> zr3644_24_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-lncRNA <==\n", "NC_047559.1\t10270\t10272\n", "NC_047559.1\t10292\t10294\n", "NC_047559.1\t10314\t10316\n", "NC_047559.1\t10545\t10547\n", "NC_047559.1\t10567\t10569\n", "NC_047559.1\t10592\t10594\n", "NC_047559.1\t10612\t10614\n", "NC_047559.1\t10667\t10669\n", "NC_047559.1\t10772\t10774\n", "NC_047559.1\t10845\t10847\n", "\n", "==> zr3644_2_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-lncRNA <==\n", "NC_047559.1\t1664658\t1664660\n", "NC_047559.1\t1664745\t1664747\n", "NC_047559.1\t1664773\t1664775\n", "NC_047559.1\t3828724\t3828726\n", "NC_047559.1\t3828793\t3828795\n", "NC_047559.1\t3829511\t3829513\n", "NC_047559.1\t3829591\t3829593\n", "NC_047559.1\t3829807\t3829809\n", "NC_047559.1\t3829827\t3829829\n", "NC_047559.1\t3829837\t3829839\n", "\n", "==> zr3644_2_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-lncRNA <==\n", "NC_047559.1\t10501\t10503\n", "NC_047559.1\t10772\t10774\n", "NC_047559.1\t10845\t10847\n", "NC_047559.1\t11026\t11028\n", "NC_047559.1\t416920\t416922\n", "NC_047559.1\t419514\t419516\n", "NC_047559.1\t1246934\t1246936\n", "NC_047559.1\t1664902\t1664904\n", "NC_047559.1\t2134319\t2134321\n", "NC_047559.1\t2139274\t2139276\n", "\n", "==> zr3644_2_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-lncRNA <==\n", "NC_047559.1\t10155\t10157\n", "NC_047559.1\t10270\t10272\n", "NC_047559.1\t10292\t10294\n", "NC_047559.1\t10314\t10316\n", "NC_047559.1\t10358\t10360\n", "NC_047559.1\t10380\t10382\n", "NC_047559.1\t10391\t10393\n", "NC_047559.1\t10402\t10404\n", "NC_047559.1\t10413\t10415\n", "NC_047559.1\t10457\t10459\n", "\n", "==> zr3644_3_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-lncRNA <==\n", "NC_047559.1\t415945\t415947\n", "NC_047559.1\t415957\t415959\n", "NC_047559.1\t415975\t415977\n", "NC_047559.1\t415988\t415990\n", "NC_047559.1\t415998\t416000\n", "NC_047559.1\t1213726\t1213728\n", "NC_047559.1\t1213731\t1213733\n", "NC_047559.1\t1664658\t1664660\n", "NC_047559.1\t1664745\t1664747\n", "NC_047559.1\t1664773\t1664775\n", "\n", "==> zr3644_3_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-lncRNA <==\n", "NC_047559.1\t227983\t227985\n", "NC_047559.1\t419514\t419516\n", "NC_047559.1\t786654\t786656\n", "NC_047559.1\t786836\t786838\n", "NC_047559.1\t788914\t788916\n", "NC_047559.1\t788918\t788920\n", "NC_047559.1\t788951\t788953\n", "NC_047559.1\t789381\t789383\n", "NC_047559.1\t1664902\t1664904\n", "NC_047559.1\t1688423\t1688425\n", "\n", "==> zr3644_3_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-lncRNA <==\n", "NC_047559.1\t10215\t10217\n", "NC_047559.1\t10270\t10272\n", "NC_047559.1\t10292\t10294\n", "NC_047559.1\t10314\t10316\n", "NC_047559.1\t10358\t10360\n", "NC_047559.1\t10402\t10404\n", "NC_047559.1\t10413\t10415\n", "NC_047559.1\t10457\t10459\n", "NC_047559.1\t10479\t10481\n", "NC_047559.1\t10501\t10503\n", "\n", "==> zr3644_4_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-lncRNA <==\n", "NC_047559.1\t415822\t415824\n", "NC_047559.1\t415998\t416000\n", "NC_047559.1\t1213812\t1213814\n", "NC_047559.1\t1664457\t1664459\n", "NC_047559.1\t1664658\t1664660\n", "NC_047559.1\t1664745\t1664747\n", "NC_047559.1\t1664773\t1664775\n", "NC_047559.1\t1664902\t1664904\n", "NC_047559.1\t1665013\t1665015\n", "NC_047559.1\t1665111\t1665113\n", "\n", "==> zr3644_4_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-lncRNA <==\n", "NC_047559.1\t10479\t10481\n", "NC_047559.1\t417337\t417339\n", "NC_047559.1\t419473\t419475\n", "NC_047559.1\t419514\t419516\n", "NC_047559.1\t788970\t788972\n", "NC_047559.1\t789309\t789311\n", "NC_047559.1\t789448\t789450\n", "NC_047559.1\t789488\t789490\n", "NC_047559.1\t789492\t789494\n", "NC_047559.1\t789510\t789512\n", "\n", "==> zr3644_4_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-lncRNA <==\n", "NC_047559.1\t10155\t10157\n", "NC_047559.1\t10270\t10272\n", "NC_047559.1\t10292\t10294\n", "NC_047559.1\t10314\t10316\n", "NC_047559.1\t10358\t10360\n", "NC_047559.1\t10501\t10503\n", "NC_047559.1\t10545\t10547\n", "NC_047559.1\t10547\t10549\n", "NC_047559.1\t10567\t10569\n", "NC_047559.1\t10592\t10594\n", "\n", "==> zr3644_5_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-lncRNA <==\n", "NC_047559.1\t418582\t418584\n", "NC_047559.1\t418592\t418594\n", "NC_047559.1\t1664745\t1664747\n", "NC_047559.1\t1664773\t1664775\n", "NC_047559.1\t2133589\t2133591\n", "NC_047559.1\t2198406\t2198408\n", "NC_047559.1\t3828724\t3828726\n", "NC_047559.1\t3829511\t3829513\n", "NC_047559.1\t3829591\t3829593\n", "NC_047559.1\t3829843\t3829845\n", "\n", "==> zr3644_5_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-lncRNA <==\n", "NC_047559.1\t416702\t416704\n", "NC_047559.1\t416757\t416759\n", "NC_047559.1\t416920\t416922\n", "NC_047559.1\t418646\t418648\n", "NC_047559.1\t419514\t419516\n", "NC_047559.1\t419784\t419786\n", "NC_047559.1\t421089\t421091\n", "NC_047559.1\t788554\t788556\n", "NC_047559.1\t1213726\t1213728\n", "NC_047559.1\t1213731\t1213733\n", "\n", "==> zr3644_5_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-lncRNA <==\n", "NC_047559.1\t10155\t10157\n", "NC_047559.1\t10215\t10217\n", "NC_047559.1\t10270\t10272\n", "NC_047559.1\t10292\t10294\n", "NC_047559.1\t10314\t10316\n", "NC_047559.1\t10358\t10360\n", "NC_047559.1\t10402\t10404\n", "NC_047559.1\t10413\t10415\n", "NC_047559.1\t10457\t10459\n", "NC_047559.1\t10479\t10481\n", "\n", "==> zr3644_6_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-lncRNA <==\n", "NC_047559.1\t419606\t419608\n", "NC_047559.1\t419784\t419786\n", "NC_047559.1\t1664658\t1664660\n", "NC_047559.1\t1664745\t1664747\n", "NC_047559.1\t1664773\t1664775\n", "NC_047559.1\t1664902\t1664904\n", "NC_047559.1\t3828724\t3828726\n", "NC_047559.1\t3828793\t3828795\n", "NC_047559.1\t3829511\t3829513\n", "NC_047559.1\t3829591\t3829593\n", "\n", "==> zr3644_6_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-lncRNA <==\n", "NC_047559.1\t242606\t242608\n", "NC_047559.1\t416757\t416759\n", "NC_047559.1\t416920\t416922\n", "NC_047559.1\t419514\t419516\n", "NC_047559.1\t419933\t419935\n", "NC_047559.1\t786947\t786949\n", "NC_047559.1\t788889\t788891\n", "NC_047559.1\t788914\t788916\n", "NC_047559.1\t788918\t788920\n", "NC_047559.1\t788943\t788945\n", "\n", "==> zr3644_6_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-lncRNA <==\n", "NC_047559.1\t10155\t10157\n", "NC_047559.1\t10215\t10217\n", "NC_047559.1\t10270\t10272\n", "NC_047559.1\t10292\t10294\n", "NC_047559.1\t10314\t10316\n", "NC_047559.1\t10457\t10459\n", "NC_047559.1\t10479\t10481\n", "NC_047559.1\t10501\t10503\n", "NC_047559.1\t10545\t10547\n", "NC_047559.1\t10547\t10549\n", "\n", "==> zr3644_7_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-lncRNA <==\n", "NC_047559.1\t415945\t415947\n", "NC_047559.1\t415957\t415959\n", "NC_047559.1\t415975\t415977\n", "NC_047559.1\t415998\t416000\n", "NC_047559.1\t416071\t416073\n", "NC_047559.1\t416088\t416090\n", "NC_047559.1\t419587\t419589\n", "NC_047559.1\t419784\t419786\n", "NC_047559.1\t1213726\t1213728\n", "NC_047559.1\t1213731\t1213733\n", "\n", "==> zr3644_7_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-lncRNA <==\n", "NC_047559.1\t10380\t10382\n", "NC_047559.1\t415988\t415990\n", "NC_047559.1\t416052\t416054\n", "NC_047559.1\t416078\t416080\n", "NC_047559.1\t416879\t416881\n", "NC_047559.1\t416920\t416922\n", "NC_047559.1\t418447\t418449\n", "NC_047559.1\t418539\t418541\n", "NC_047559.1\t418551\t418553\n", "NC_047559.1\t418569\t418571\n", "\n", "==> zr3644_7_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-lncRNA <==\n", "NC_047559.1\t10155\t10157\n", "NC_047559.1\t10215\t10217\n", "NC_047559.1\t10270\t10272\n", "NC_047559.1\t10292\t10294\n", "NC_047559.1\t10314\t10316\n", "NC_047559.1\t10358\t10360\n", "NC_047559.1\t10391\t10393\n", "NC_047559.1\t10402\t10404\n", "NC_047559.1\t10413\t10415\n", "NC_047559.1\t10457\t10459\n", "\n", "==> zr3644_8_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-lncRNA <==\n", "NC_047559.1\t1664658\t1664660\n", "NC_047559.1\t1664745\t1664747\n", "NC_047559.1\t1664773\t1664775\n", "NC_047559.1\t1665013\t1665015\n", "NC_047559.1\t1665259\t1665261\n", "NC_047559.1\t3828724\t3828726\n", "NC_047559.1\t3828793\t3828795\n", "NC_047559.1\t3829511\t3829513\n", "NC_047559.1\t3829591\t3829593\n", "NC_047559.1\t3829807\t3829809\n", "\n", "==> zr3644_8_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-lncRNA <==\n", "NC_047559.1\t1248102\t1248104\n", "NC_047559.1\t1248111\t1248113\n", "NC_047559.1\t1248722\t1248724\n", "NC_047559.1\t2133510\t2133512\n", "NC_047559.1\t2133616\t2133618\n", "NC_047559.1\t2140446\t2140448\n", "NC_047559.1\t2198406\t2198408\n", "NC_047559.1\t2199691\t2199693\n", "NC_047559.1\t2297310\t2297312\n", "NC_047559.1\t3029336\t3029338\n", "\n", "==> zr3644_8_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-lncRNA <==\n", "NC_047559.1\t10270\t10272\n", "NC_047559.1\t10292\t10294\n", "NC_047559.1\t10314\t10316\n", "NC_047559.1\t10413\t10415\n", "NC_047559.1\t10457\t10459\n", "NC_047559.1\t10479\t10481\n", "NC_047559.1\t10501\t10503\n", "NC_047559.1\t10545\t10547\n", "NC_047559.1\t10547\t10549\n", "NC_047559.1\t10567\t10569\n", "\n", "==> zr3644_9_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-lncRNA <==\n", "NC_047559.1\t417944\t417946\n", "NC_047559.1\t419514\t419516\n", "NC_047559.1\t419784\t419786\n", "NC_047559.1\t420583\t420585\n", "NC_047559.1\t420980\t420982\n", "NC_047559.1\t1213726\t1213728\n", "NC_047559.1\t1213731\t1213733\n", "NC_047559.1\t1664773\t1664775\n", "NC_047559.1\t1688466\t1688468\n", "NC_047559.1\t3828724\t3828726\n", "\n", "==> zr3644_9_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-lncRNA <==\n", "NC_047559.1\t416879\t416881\n", "NC_047559.1\t416920\t416922\n", "NC_047559.1\t416993\t416995\n", "NC_047559.1\t417012\t417014\n", "NC_047559.1\t418592\t418594\n", "NC_047559.1\t418646\t418648\n", "NC_047559.1\t418665\t418667\n", "NC_047559.1\t418672\t418674\n", "NC_047559.1\t419473\t419475\n", "NC_047559.1\t419933\t419935\n", "\n", "==> zr3644_9_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-lncRNA <==\n", "NC_047559.1\t10391\t10393\n", "NC_047559.1\t10402\t10404\n", "NC_047559.1\t10413\t10415\n", "NC_047559.1\t10845\t10847\n", "NC_047559.1\t10859\t10861\n", "NC_047559.1\t10899\t10901\n", "NC_047559.1\t10920\t10922\n", "NC_047559.1\t10950\t10952\n", "NC_047559.1\t11000\t11002\n", "NC_047559.1\t226734\t226736\n", "\n", "==> zr3644_union-averages_5x.bedgraph-Meth.bed-lncRNA <==\n", "NC_047559.1\t417944\t417946\n", "NC_047559.1\t420980\t420982\n", "NC_047559.1\t1214656\t1214658\n", "NC_047559.1\t1215016\t1215018\n", "NC_047559.1\t1664457\t1664459\n", "NC_047559.1\t1664587\t1664589\n", "NC_047559.1\t1664658\t1664660\n", "NC_047559.1\t1664745\t1664747\n", "NC_047559.1\t1664773\t1664775\n", "NC_047559.1\t1665013\t1665015\n", "\n", "==> zr3644_union-averages_5x.bedgraph-sparseMeth.bed-lncRNA <==\n", "NC_047559.1\t228525\t228527\n", "NC_047559.1\t255789\t255791\n", "NC_047559.1\t415714\t415716\n", "NC_047559.1\t415739\t415741\n", "NC_047559.1\t415822\t415824\n", "NC_047559.1\t415945\t415947\n", "NC_047559.1\t415957\t415959\n", "NC_047559.1\t415975\t415977\n", "NC_047559.1\t415988\t415990\n", "NC_047559.1\t415998\t416000\n", "\n", "==> zr3644_union-averages_5x.bedgraph-unMeth.bed-lncRNA <==\n", "NC_047559.1\t10155\t10157\n", "NC_047559.1\t10215\t10217\n", "NC_047559.1\t10270\t10272\n", "NC_047559.1\t10292\t10294\n", "NC_047559.1\t10314\t10316\n", "NC_047559.1\t10358\t10360\n", "NC_047559.1\t10380\t10382\n", "NC_047559.1\t10391\t10393\n", "NC_047559.1\t10402\t10404\n", "NC_047559.1\t10413\t10415\n" ] } ], "source": [ "#Check output\n", "!head *lncRNA" ] }, { "cell_type": "code", "execution_count": 69, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ " 11815 zr3644_10_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-lncRNA\n", " 19718 zr3644_10_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-lncRNA\n", " 167405 zr3644_10_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-lncRNA\n", " 11896 zr3644_11_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-lncRNA\n", " 20834 zr3644_11_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-lncRNA\n", " 176096 zr3644_11_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-lncRNA\n", " 10290 zr3644_12_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-lncRNA\n", " 18038 zr3644_12_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-lncRNA\n", " 163933 zr3644_12_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-lncRNA\n", " 11791 zr3644_13_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-lncRNA\n", " 21620 zr3644_13_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-lncRNA\n", " 173954 zr3644_13_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-lncRNA\n", " 13203 zr3644_14_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-lncRNA\n", " 13344 zr3644_14_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-lncRNA\n", " 128973 zr3644_14_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-lncRNA\n", " 14384 zr3644_15_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-lncRNA\n", " 22378 zr3644_15_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-lncRNA\n", " 180301 zr3644_15_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-lncRNA\n", " 11078 zr3644_16_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-lncRNA\n", " 18539 zr3644_16_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-lncRNA\n", " 159032 zr3644_16_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-lncRNA\n", " 12391 zr3644_17_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-lncRNA\n", " 18497 zr3644_17_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-lncRNA\n", " 173289 zr3644_17_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-lncRNA\n", " 11056 zr3644_18_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-lncRNA\n", " 19688 zr3644_18_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-lncRNA\n", " 162946 zr3644_18_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-lncRNA\n", " 10741 zr3644_19_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-lncRNA\n", " 18803 zr3644_19_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-lncRNA\n", " 161623 zr3644_19_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-lncRNA\n", " 9676 zr3644_1_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-lncRNA\n", " 18832 zr3644_1_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-lncRNA\n", " 160236 zr3644_1_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-lncRNA\n", " 11155 zr3644_20_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-lncRNA\n", " 20346 zr3644_20_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-lncRNA\n", " 172458 zr3644_20_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-lncRNA\n", " 11443 zr3644_21_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-lncRNA\n", " 20504 zr3644_21_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-lncRNA\n", " 169088 zr3644_21_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-lncRNA\n", " 10403 zr3644_22_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-lncRNA\n", " 17960 zr3644_22_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-lncRNA\n", " 156585 zr3644_22_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-lncRNA\n", " 9190 zr3644_23_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-lncRNA\n", " 16697 zr3644_23_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-lncRNA\n", " 139625 zr3644_23_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-lncRNA\n", " 11211 zr3644_24_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-lncRNA\n", " 19655 zr3644_24_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-lncRNA\n", " 167327 zr3644_24_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-lncRNA\n", " 12960 zr3644_2_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-lncRNA\n", " 18001 zr3644_2_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-lncRNA\n", " 177225 zr3644_2_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-lncRNA\n", " 9753 zr3644_3_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-lncRNA\n", " 16924 zr3644_3_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-lncRNA\n", " 141828 zr3644_3_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-lncRNA\n", " 10440 zr3644_4_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-lncRNA\n", " 19057 zr3644_4_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-lncRNA\n", " 166205 zr3644_4_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-lncRNA\n", " 10317 zr3644_5_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-lncRNA\n", " 18370 zr3644_5_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-lncRNA\n", " 153662 zr3644_5_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-lncRNA\n", " 11276 zr3644_6_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-lncRNA\n", " 19537 zr3644_6_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-lncRNA\n", " 170102 zr3644_6_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-lncRNA\n", " 14740 zr3644_7_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-lncRNA\n", " 25028 zr3644_7_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-lncRNA\n", " 213510 zr3644_7_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-lncRNA\n", " 10558 zr3644_8_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-lncRNA\n", " 17853 zr3644_8_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-lncRNA\n", " 149892 zr3644_8_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-lncRNA\n", " 10982 zr3644_9_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-lncRNA\n", " 18258 zr3644_9_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-lncRNA\n", " 149401 zr3644_9_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-lncRNA\n", " 17023 zr3644_union-averages_5x.bedgraph-Meth.bed-lncRNA\n", " 35974 zr3644_union-averages_5x.bedgraph-sparseMeth.bed-lncRNA\n", " 289710 zr3644_union-averages_5x.bedgraph-unMeth.bed-lncRNA\n", " 5008633 total\n" ] } ], "source": [ "#Count number of overlaps\n", "!wc -l *lncRNA" ] }, { "cell_type": "code", "execution_count": 70, "metadata": { "collapsed": true }, "outputs": [], "source": [ "#Get line counts for each fine\n", "# Remove 28th line (total entries)\n", "#Ensure output is tab-delimited\n", "#Save output\n", "!wc -l *-lncRNA \\\n", "| sed '76,$ d' \\\n", "| awk '{print $1\"\\t\"$2}' \\\n", "> zr3644_5x-lncRNA-counts.txt" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "### 6j. Transposable elements" ] }, { "cell_type": "code", "execution_count": 71, "metadata": { "collapsed": false }, "outputs": [], "source": [ "%%bash\n", "for f in *bed\n", "do\n", " /Users/Shared/bioinformatics/bedtools2/bin/intersectBed \\\n", " -u \\\n", " -a ${f} \\\n", " -b /Volumes/web-1/halfshell/genomic-databank/cgigas_uk_roslin_v1_rm.te.bed \\\n", " > ${f}-TE\n", "done" ] }, { "cell_type": "code", "execution_count": 72, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "==> zr3644_10_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-TE <==\n", "NC_047559.1\t344549\t344551\n", "NC_047559.1\t344803\t344805\n", "NC_047559.1\t344812\t344814\n", "NC_047559.1\t356335\t356337\n", "NC_047559.1\t356436\t356438\n", "NC_047559.1\t356685\t356687\n", "NC_047559.1\t357799\t357801\n", "NC_047559.1\t357900\t357902\n", "NC_047559.1\t357955\t357957\n", "NC_047559.1\t358313\t358315\n", "\n", "==> zr3644_10_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-TE <==\n", "NC_047559.1\t26448\t26450\n", "NC_047559.1\t26699\t26701\n", "NC_047559.1\t42362\t42364\n", "NC_047559.1\t42415\t42417\n", "NC_047559.1\t43952\t43954\n", "NC_047559.1\t51213\t51215\n", "NC_047559.1\t51242\t51244\n", "NC_047559.1\t51249\t51251\n", "NC_047559.1\t51298\t51300\n", "NC_047559.1\t51319\t51321\n", "\n", "==> zr3644_10_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-TE <==\n", "NC_047559.1\t15746\t15748\n", "NC_047559.1\t26419\t26421\n", "NC_047559.1\t26463\t26465\n", "NC_047559.1\t26485\t26487\n", "NC_047559.1\t26509\t26511\n", "NC_047559.1\t26532\t26534\n", "NC_047559.1\t26547\t26549\n", "NC_047559.1\t26555\t26557\n", "NC_047559.1\t26561\t26563\n", "NC_047559.1\t26573\t26575\n", "\n", "==> zr3644_11_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-TE <==\n", "NC_047559.1\t139898\t139900\n", "NC_047559.1\t139912\t139914\n", "NC_047559.1\t139926\t139928\n", "NC_047559.1\t139945\t139947\n", "NC_047559.1\t139954\t139956\n", "NC_047559.1\t139972\t139974\n", "NC_047559.1\t139998\t140000\n", "NC_047559.1\t140007\t140009\n", "NC_047559.1\t140046\t140048\n", "NC_047559.1\t141777\t141779\n", "\n", "==> zr3644_11_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-TE <==\n", "NC_047559.1\t32492\t32494\n", "NC_047559.1\t41242\t41244\n", "NC_047559.1\t49957\t49959\n", "NC_047559.1\t49963\t49965\n", "NC_047559.1\t51037\t51039\n", "NC_047559.1\t51099\t51101\n", "NC_047559.1\t56231\t56233\n", "NC_047559.1\t61203\t61205\n", "NC_047559.1\t62770\t62772\n", "NC_047559.1\t68070\t68072\n", "\n", "==> zr3644_11_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-TE <==\n", "NC_047559.1\t15746\t15748\n", "NC_047559.1\t26419\t26421\n", "NC_047559.1\t26448\t26450\n", "NC_047559.1\t26463\t26465\n", "NC_047559.1\t26485\t26487\n", "NC_047559.1\t26509\t26511\n", "NC_047559.1\t26532\t26534\n", "NC_047559.1\t26547\t26549\n", "NC_047559.1\t26555\t26557\n", "NC_047559.1\t26561\t26563\n", "\n", "==> zr3644_12_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-TE <==\n", "NC_047559.1\t141751\t141753\n", "NC_047559.1\t141777\t141779\n", "NC_047559.1\t350782\t350784\n", "NC_047559.1\t350848\t350850\n", "NC_047559.1\t350948\t350950\n", "NC_047559.1\t424694\t424696\n", "NC_047559.1\t425403\t425405\n", "NC_047559.1\t425491\t425493\n", "NC_047559.1\t425516\t425518\n", "NC_047559.1\t425580\t425582\n", "\n", "==> zr3644_12_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-TE <==\n", "NC_047559.1\t26419\t26421\n", "NC_047559.1\t26448\t26450\n", "NC_047559.1\t26699\t26701\n", "NC_047559.1\t27143\t27145\n", "NC_047559.1\t35954\t35956\n", "NC_047559.1\t39405\t39407\n", "NC_047559.1\t42415\t42417\n", "NC_047559.1\t45403\t45405\n", "NC_047559.1\t49264\t49266\n", "NC_047559.1\t49314\t49316\n", "\n", "==> zr3644_12_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-TE <==\n", "NC_047559.1\t15746\t15748\n", "NC_047559.1\t26509\t26511\n", "NC_047559.1\t26532\t26534\n", "NC_047559.1\t26547\t26549\n", "NC_047559.1\t26555\t26557\n", "NC_047559.1\t26561\t26563\n", "NC_047559.1\t26573\t26575\n", "NC_047559.1\t26591\t26593\n", "NC_047559.1\t26593\t26595\n", "NC_047559.1\t26648\t26650\n", "\n", "==> zr3644_13_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-TE <==\n", "NC_047559.1\t26699\t26701\n", "NC_047559.1\t139998\t140000\n", "NC_047559.1\t140007\t140009\n", "NC_047559.1\t194178\t194180\n", "NC_047559.1\t194293\t194295\n", "NC_047559.1\t338430\t338432\n", "NC_047559.1\t356335\t356337\n", "NC_047559.1\t356748\t356750\n", "NC_047559.1\t357784\t357786\n", "NC_047559.1\t357799\t357801\n", "\n", "==> zr3644_13_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-TE <==\n", "NC_047559.1\t26448\t26450\n", "NC_047559.1\t26677\t26679\n", "NC_047559.1\t26738\t26740\n", "NC_047559.1\t26746\t26748\n", "NC_047559.1\t27193\t27195\n", "NC_047559.1\t27557\t27559\n", "NC_047559.1\t33190\t33192\n", "NC_047559.1\t33210\t33212\n", "NC_047559.1\t33576\t33578\n", "NC_047559.1\t44421\t44423\n", "\n", "==> zr3644_13_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-TE <==\n", "NC_047559.1\t15746\t15748\n", "NC_047559.1\t26419\t26421\n", "NC_047559.1\t26463\t26465\n", "NC_047559.1\t26485\t26487\n", "NC_047559.1\t26509\t26511\n", "NC_047559.1\t26532\t26534\n", "NC_047559.1\t26547\t26549\n", "NC_047559.1\t26555\t26557\n", "NC_047559.1\t26561\t26563\n", "NC_047559.1\t26573\t26575\n", "\n", "==> zr3644_14_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-TE <==\n", "NC_047559.1\t62770\t62772\n", "NC_047559.1\t68070\t68072\n", "NC_047559.1\t164604\t164606\n", "NC_047559.1\t164626\t164628\n", "NC_047559.1\t164628\t164630\n", "NC_047559.1\t164642\t164644\n", "NC_047559.1\t164647\t164649\n", "NC_047559.1\t164662\t164664\n", "NC_047559.1\t299369\t299371\n", "NC_047559.1\t344549\t344551\n", "\n", "==> zr3644_14_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-TE <==\n", "NC_047559.1\t31135\t31137\n", "NC_047559.1\t33595\t33597\n", "NC_047559.1\t41242\t41244\n", "NC_047559.1\t50492\t50494\n", "NC_047559.1\t56037\t56039\n", "NC_047559.1\t56073\t56075\n", "NC_047559.1\t56090\t56092\n", "NC_047559.1\t56231\t56233\n", "NC_047559.1\t60430\t60432\n", "NC_047559.1\t61081\t61083\n", "\n", "==> zr3644_14_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-TE <==\n", "NC_047559.1\t15746\t15748\n", "NC_047559.1\t25667\t25669\n", "NC_047559.1\t27324\t27326\n", "NC_047559.1\t27410\t27412\n", "NC_047559.1\t27420\t27422\n", "NC_047559.1\t27429\t27431\n", "NC_047559.1\t27557\t27559\n", "NC_047559.1\t30977\t30979\n", "NC_047559.1\t31019\t31021\n", "NC_047559.1\t31051\t31053\n", "\n", "==> zr3644_15_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-TE <==\n", "NC_047559.1\t139972\t139974\n", "NC_047559.1\t139998\t140000\n", "NC_047559.1\t140007\t140009\n", "NC_047559.1\t140046\t140048\n", "NC_047559.1\t140539\t140541\n", "NC_047559.1\t140557\t140559\n", "NC_047559.1\t140589\t140591\n", "NC_047559.1\t140640\t140642\n", "NC_047559.1\t141708\t141710\n", "NC_047559.1\t141751\t141753\n", "\n", "==> zr3644_15_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-TE <==\n", "NC_047559.1\t26746\t26748\n", "NC_047559.1\t30665\t30667\n", "NC_047559.1\t30680\t30682\n", "NC_047559.1\t38052\t38054\n", "NC_047559.1\t46678\t46680\n", "NC_047559.1\t47777\t47779\n", "NC_047559.1\t47794\t47796\n", "NC_047559.1\t50022\t50024\n", "NC_047559.1\t50083\t50085\n", "NC_047559.1\t50500\t50502\n", "\n", "==> zr3644_15_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-TE <==\n", "NC_047559.1\t15746\t15748\n", "NC_047559.1\t25485\t25487\n", "NC_047559.1\t25667\t25669\n", "NC_047559.1\t26135\t26137\n", "NC_047559.1\t26419\t26421\n", "NC_047559.1\t26448\t26450\n", "NC_047559.1\t26463\t26465\n", "NC_047559.1\t26485\t26487\n", "NC_047559.1\t26509\t26511\n", "NC_047559.1\t26532\t26534\n", "\n", "==> zr3644_16_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-TE <==\n", "NC_047559.1\t276024\t276026\n", "NC_047559.1\t335850\t335852\n", "NC_047559.1\t335858\t335860\n", "NC_047559.1\t338777\t338779\n", "NC_047559.1\t338819\t338821\n", "NC_047559.1\t338862\t338864\n", "NC_047559.1\t338883\t338885\n", "NC_047559.1\t339095\t339097\n", "NC_047559.1\t341533\t341535\n", "NC_047559.1\t341535\t341537\n", "\n", "==> zr3644_16_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-TE <==\n", "NC_047559.1\t37587\t37589\n", "NC_047559.1\t45248\t45250\n", "NC_047559.1\t46678\t46680\n", "NC_047559.1\t56037\t56039\n", "NC_047559.1\t56073\t56075\n", "NC_047559.1\t56090\t56092\n", "NC_047559.1\t62770\t62772\n", "NC_047559.1\t132290\t132292\n", "NC_047559.1\t139430\t139432\n", "NC_047559.1\t139438\t139440\n", "\n", "==> zr3644_16_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-TE <==\n", "NC_047559.1\t15746\t15748\n", "NC_047559.1\t26419\t26421\n", "NC_047559.1\t26448\t26450\n", "NC_047559.1\t26463\t26465\n", "NC_047559.1\t26509\t26511\n", "NC_047559.1\t26532\t26534\n", "NC_047559.1\t26547\t26549\n", "NC_047559.1\t26555\t26557\n", "NC_047559.1\t26561\t26563\n", "NC_047559.1\t26573\t26575\n", "\n", "==> zr3644_17_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-TE <==\n", "NC_047559.1\t44918\t44920\n", "NC_047559.1\t147333\t147335\n", "NC_047559.1\t147335\t147337\n", "NC_047559.1\t194307\t194309\n", "NC_047559.1\t231888\t231890\n", "NC_047559.1\t288667\t288669\n", "NC_047559.1\t292774\t292776\n", "NC_047559.1\t292780\t292782\n", "NC_047559.1\t292794\t292796\n", "NC_047559.1\t294825\t294827\n", "\n", "==> zr3644_17_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-TE <==\n", "NC_047559.1\t25485\t25487\n", "NC_047559.1\t31135\t31137\n", "NC_047559.1\t45010\t45012\n", "NC_047559.1\t46740\t46742\n", "NC_047559.1\t49042\t49044\n", "NC_047559.1\t49867\t49869\n", "NC_047559.1\t50869\t50871\n", "NC_047559.1\t50878\t50880\n", "NC_047559.1\t50885\t50887\n", "NC_047559.1\t50890\t50892\n", "\n", "==> zr3644_17_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-TE <==\n", "NC_047559.1\t15746\t15748\n", "NC_047559.1\t26463\t26465\n", "NC_047559.1\t26485\t26487\n", "NC_047559.1\t26509\t26511\n", "NC_047559.1\t26532\t26534\n", "NC_047559.1\t26547\t26549\n", "NC_047559.1\t26555\t26557\n", "NC_047559.1\t26561\t26563\n", "NC_047559.1\t26573\t26575\n", "NC_047559.1\t26591\t26593\n", "\n", "==> zr3644_18_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-TE <==\n", "NC_047559.1\t26787\t26789\n", "NC_047559.1\t139972\t139974\n", "NC_047559.1\t139998\t140000\n", "NC_047559.1\t140007\t140009\n", "NC_047559.1\t140046\t140048\n", "NC_047559.1\t140520\t140522\n", "NC_047559.1\t140539\t140541\n", "NC_047559.1\t140557\t140559\n", "NC_047559.1\t140589\t140591\n", "NC_047559.1\t140640\t140642\n", "\n", "==> zr3644_18_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-TE <==\n", "NC_047559.1\t26699\t26701\n", "NC_047559.1\t26738\t26740\n", "NC_047559.1\t26746\t26748\n", "NC_047559.1\t31986\t31988\n", "NC_047559.1\t33534\t33536\n", "NC_047559.1\t41242\t41244\n", "NC_047559.1\t42410\t42412\n", "NC_047559.1\t42415\t42417\n", "NC_047559.1\t42690\t42692\n", "NC_047559.1\t43644\t43646\n", "\n", "==> zr3644_18_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-TE <==\n", "NC_047559.1\t15746\t15748\n", "NC_047559.1\t26419\t26421\n", "NC_047559.1\t26448\t26450\n", "NC_047559.1\t26463\t26465\n", "NC_047559.1\t26485\t26487\n", "NC_047559.1\t26509\t26511\n", "NC_047559.1\t26532\t26534\n", "NC_047559.1\t26547\t26549\n", "NC_047559.1\t26555\t26557\n", "NC_047559.1\t26561\t26563\n", "\n", "==> zr3644_19_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-TE <==\n", "NC_047559.1\t56073\t56075\n", "NC_047559.1\t56090\t56092\n", "NC_047559.1\t140894\t140896\n", "NC_047559.1\t141800\t141802\n", "NC_047559.1\t141853\t141855\n", "NC_047559.1\t141858\t141860\n", "NC_047559.1\t142531\t142533\n", "NC_047559.1\t142545\t142547\n", "NC_047559.1\t147333\t147335\n", "NC_047559.1\t147335\t147337\n", "\n", "==> zr3644_19_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-TE <==\n", "NC_047559.1\t32640\t32642\n", "NC_047559.1\t33210\t33212\n", "NC_047559.1\t35713\t35715\n", "NC_047559.1\t42696\t42698\n", "NC_047559.1\t44220\t44222\n", "NC_047559.1\t51178\t51180\n", "NC_047559.1\t51317\t51319\n", "NC_047559.1\t51319\t51321\n", "NC_047559.1\t62770\t62772\n", "NC_047559.1\t83475\t83477\n", "\n", "==> zr3644_19_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-TE <==\n", "NC_047559.1\t15746\t15748\n", "NC_047559.1\t26419\t26421\n", "NC_047559.1\t26448\t26450\n", "NC_047559.1\t26463\t26465\n", "NC_047559.1\t26485\t26487\n", "NC_047559.1\t26509\t26511\n", "NC_047559.1\t26532\t26534\n", "NC_047559.1\t26547\t26549\n", "NC_047559.1\t26555\t26557\n", "NC_047559.1\t26561\t26563\n", "\n", "==> zr3644_1_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-TE <==\n", "NC_047559.1\t68070\t68072\n", "NC_047559.1\t231691\t231693\n", "NC_047559.1\t262768\t262770\n", "NC_047559.1\t262797\t262799\n", "NC_047559.1\t276024\t276026\n", "NC_047559.1\t293474\t293476\n", "NC_047559.1\t294921\t294923\n", "NC_047559.1\t294966\t294968\n", "NC_047559.1\t294970\t294972\n", "NC_047559.1\t294988\t294990\n", "\n", "==> zr3644_1_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-TE <==\n", "NC_047559.1\t26509\t26511\n", "NC_047559.1\t26561\t26563\n", "NC_047559.1\t26591\t26593\n", "NC_047559.1\t39537\t39539\n", "NC_047559.1\t41242\t41244\n", "NC_047559.1\t42392\t42394\n", "NC_047559.1\t42415\t42417\n", "NC_047559.1\t46646\t46648\n", "NC_047559.1\t50217\t50219\n", "NC_047559.1\t50465\t50467\n", "\n", "==> zr3644_1_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-TE <==\n", "NC_047559.1\t15746\t15748\n", "NC_047559.1\t26532\t26534\n", "NC_047559.1\t26547\t26549\n", "NC_047559.1\t26555\t26557\n", "NC_047559.1\t26573\t26575\n", "NC_047559.1\t26593\t26595\n", "NC_047559.1\t26648\t26650\n", "NC_047559.1\t26651\t26653\n", "NC_047559.1\t26677\t26679\n", "NC_047559.1\t27324\t27326\n", "\n", "==> zr3644_20_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-TE <==\n", "NC_047559.1\t60313\t60315\n", "NC_047559.1\t60371\t60373\n", "NC_047559.1\t319341\t319343\n", "NC_047559.1\t319399\t319401\n", "NC_047559.1\t319408\t319410\n", "NC_047559.1\t350973\t350975\n", "NC_047559.1\t351006\t351008\n", "NC_047559.1\t416920\t416922\n", "NC_047559.1\t425255\t425257\n", "NC_047559.1\t425403\t425405\n", "\n", "==> zr3644_20_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-TE <==\n", "NC_047559.1\t26419\t26421\n", "NC_047559.1\t26448\t26450\n", "NC_047559.1\t26677\t26679\n", "NC_047559.1\t26699\t26701\n", "NC_047559.1\t26738\t26740\n", "NC_047559.1\t33120\t33122\n", "NC_047559.1\t39520\t39522\n", "NC_047559.1\t44113\t44115\n", "NC_047559.1\t46740\t46742\n", "NC_047559.1\t49365\t49367\n", "\n", "==> zr3644_20_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-TE <==\n", "NC_047559.1\t15746\t15748\n", "NC_047559.1\t26463\t26465\n", "NC_047559.1\t26485\t26487\n", "NC_047559.1\t26509\t26511\n", "NC_047559.1\t26532\t26534\n", "NC_047559.1\t26547\t26549\n", "NC_047559.1\t26555\t26557\n", "NC_047559.1\t26561\t26563\n", "NC_047559.1\t26573\t26575\n", "NC_047559.1\t26591\t26593\n", "\n", "==> zr3644_21_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-TE <==\n", "NC_047559.1\t141853\t141855\n", "NC_047559.1\t141858\t141860\n", "NC_047559.1\t142447\t142449\n", "NC_047559.1\t142465\t142467\n", "NC_047559.1\t142484\t142486\n", "NC_047559.1\t147295\t147297\n", "NC_047559.1\t147297\t147299\n", "NC_047559.1\t147299\t147301\n", "NC_047559.1\t147307\t147309\n", "NC_047559.1\t311476\t311478\n", "\n", "==> zr3644_21_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-TE <==\n", "NC_047559.1\t27420\t27422\n", "NC_047559.1\t31019\t31021\n", "NC_047559.1\t42415\t42417\n", "NC_047559.1\t42437\t42439\n", "NC_047559.1\t42652\t42654\n", "NC_047559.1\t49031\t49033\n", "NC_047559.1\t49042\t49044\n", "NC_047559.1\t50168\t50170\n", "NC_047559.1\t56073\t56075\n", "NC_047559.1\t56082\t56084\n", "\n", "==> zr3644_21_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-TE <==\n", "NC_047559.1\t15746\t15748\n", "NC_047559.1\t26547\t26549\n", "NC_047559.1\t26555\t26557\n", "NC_047559.1\t26561\t26563\n", "NC_047559.1\t26573\t26575\n", "NC_047559.1\t26591\t26593\n", "NC_047559.1\t26593\t26595\n", "NC_047559.1\t26648\t26650\n", "NC_047559.1\t26651\t26653\n", "NC_047559.1\t26677\t26679\n", "\n", "==> zr3644_22_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-TE <==\n", "NC_047559.1\t141708\t141710\n", "NC_047559.1\t141751\t141753\n", "NC_047559.1\t141777\t141779\n", "NC_047559.1\t154324\t154326\n", "NC_047559.1\t335353\t335355\n", "NC_047559.1\t335373\t335375\n", "NC_047559.1\t335375\t335377\n", "NC_047559.1\t344440\t344442\n", "NC_047559.1\t344477\t344479\n", "NC_047559.1\t344803\t344805\n", "\n", "==> zr3644_22_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-TE <==\n", "NC_047559.1\t26463\t26465\n", "NC_047559.1\t42762\t42764\n", "NC_047559.1\t42791\t42793\n", "NC_047559.1\t46845\t46847\n", "NC_047559.1\t49031\t49033\n", "NC_047559.1\t51178\t51180\n", "NC_047559.1\t51180\t51182\n", "NC_047559.1\t51213\t51215\n", "NC_047559.1\t51242\t51244\n", "NC_047559.1\t51249\t51251\n", "\n", "==> zr3644_22_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-TE <==\n", "NC_047559.1\t15746\t15748\n", "NC_047559.1\t26419\t26421\n", "NC_047559.1\t26448\t26450\n", "NC_047559.1\t26509\t26511\n", "NC_047559.1\t26532\t26534\n", "NC_047559.1\t26547\t26549\n", "NC_047559.1\t26555\t26557\n", "NC_047559.1\t26561\t26563\n", "NC_047559.1\t26573\t26575\n", "NC_047559.1\t26591\t26593\n", "\n", "==> zr3644_23_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-TE <==\n", "NC_047559.1\t310755\t310757\n", "NC_047559.1\t310766\t310768\n", "NC_047559.1\t310826\t310828\n", "NC_047559.1\t310828\t310830\n", "NC_047559.1\t350782\t350784\n", "NC_047559.1\t350786\t350788\n", "NC_047559.1\t350807\t350809\n", "NC_047559.1\t356335\t356337\n", "NC_047559.1\t356378\t356380\n", "NC_047559.1\t356395\t356397\n", "\n", "==> zr3644_23_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-TE <==\n", "NC_047559.1\t42415\t42417\n", "NC_047559.1\t44210\t44212\n", "NC_047559.1\t44220\t44222\n", "NC_047559.1\t44230\t44232\n", "NC_047559.1\t44234\t44236\n", "NC_047559.1\t49754\t49756\n", "NC_047559.1\t51099\t51101\n", "NC_047559.1\t51249\t51251\n", "NC_047559.1\t56073\t56075\n", "NC_047559.1\t56090\t56092\n", "\n", "==> zr3644_23_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-TE <==\n", "NC_047559.1\t15746\t15748\n", "NC_047559.1\t26419\t26421\n", "NC_047559.1\t26448\t26450\n", "NC_047559.1\t26463\t26465\n", "NC_047559.1\t26485\t26487\n", "NC_047559.1\t26509\t26511\n", "NC_047559.1\t26532\t26534\n", "NC_047559.1\t26547\t26549\n", "NC_047559.1\t26555\t26557\n", "NC_047559.1\t26561\t26563\n", "\n", "==> zr3644_24_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-TE <==\n", "NC_047559.1\t37861\t37863\n", "NC_047559.1\t56073\t56075\n", "NC_047559.1\t56264\t56266\n", "NC_047559.1\t141708\t141710\n", "NC_047559.1\t141717\t141719\n", "NC_047559.1\t141751\t141753\n", "NC_047559.1\t141777\t141779\n", "NC_047559.1\t141800\t141802\n", "NC_047559.1\t309328\t309330\n", "NC_047559.1\t310854\t310856\n", "\n", "==> zr3644_24_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-TE <==\n", "NC_047559.1\t26699\t26701\n", "NC_047559.1\t26738\t26740\n", "NC_047559.1\t27132\t27134\n", "NC_047559.1\t33595\t33597\n", "NC_047559.1\t42415\t42417\n", "NC_047559.1\t43374\t43376\n", "NC_047559.1\t45033\t45035\n", "NC_047559.1\t46678\t46680\n", "NC_047559.1\t56037\t56039\n", "NC_047559.1\t56090\t56092\n", "\n", "==> zr3644_24_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-TE <==\n", "NC_047559.1\t15746\t15748\n", "NC_047559.1\t26419\t26421\n", "NC_047559.1\t26448\t26450\n", "NC_047559.1\t26463\t26465\n", "NC_047559.1\t26485\t26487\n", "NC_047559.1\t26509\t26511\n", "NC_047559.1\t26532\t26534\n", "NC_047559.1\t26547\t26549\n", "NC_047559.1\t26555\t26557\n", "NC_047559.1\t26561\t26563\n", "\n", "==> zr3644_2_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-TE <==\n", "NC_047559.1\t56073\t56075\n", "NC_047559.1\t56090\t56092\n", "NC_047559.1\t61081\t61083\n", "NC_047559.1\t292774\t292776\n", "NC_047559.1\t292788\t292790\n", "NC_047559.1\t292794\t292796\n", "NC_047559.1\t294722\t294724\n", "NC_047559.1\t294966\t294968\n", "NC_047559.1\t295657\t295659\n", "NC_047559.1\t295663\t295665\n", "\n", "==> zr3644_2_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-TE <==\n", "NC_047559.1\t37861\t37863\n", "NC_047559.1\t42591\t42593\n", "NC_047559.1\t42595\t42597\n", "NC_047559.1\t49314\t49316\n", "NC_047559.1\t50968\t50970\n", "NC_047559.1\t51037\t51039\n", "NC_047559.1\t51298\t51300\n", "NC_047559.1\t51317\t51319\n", "NC_047559.1\t51319\t51321\n", "NC_047559.1\t51469\t51471\n", "\n", "==> zr3644_2_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-TE <==\n", "NC_047559.1\t15746\t15748\n", "NC_047559.1\t26419\t26421\n", "NC_047559.1\t26448\t26450\n", "NC_047559.1\t26463\t26465\n", "NC_047559.1\t26485\t26487\n", "NC_047559.1\t26509\t26511\n", "NC_047559.1\t26532\t26534\n", "NC_047559.1\t26547\t26549\n", "NC_047559.1\t26555\t26557\n", "NC_047559.1\t26561\t26563\n", "\n", "==> zr3644_3_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-TE <==\n", "NC_047559.1\t338430\t338432\n", "NC_047559.1\t338444\t338446\n", "NC_047559.1\t338617\t338619\n", "NC_047559.1\t340912\t340914\n", "NC_047559.1\t340923\t340925\n", "NC_047559.1\t341839\t341841\n", "NC_047559.1\t342246\t342248\n", "NC_047559.1\t342250\t342252\n", "NC_047559.1\t344549\t344551\n", "NC_047559.1\t350807\t350809\n", "\n", "==> zr3644_3_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-TE <==\n", "NC_047559.1\t26955\t26957\n", "NC_047559.1\t38030\t38032\n", "NC_047559.1\t42499\t42501\n", "NC_047559.1\t42696\t42698\n", "NC_047559.1\t42709\t42711\n", "NC_047559.1\t49575\t49577\n", "NC_047559.1\t49754\t49756\n", "NC_047559.1\t51099\t51101\n", "NC_047559.1\t51178\t51180\n", "NC_047559.1\t51180\t51182\n", "\n", "==> zr3644_3_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-TE <==\n", "NC_047559.1\t15746\t15748\n", "NC_047559.1\t26419\t26421\n", "NC_047559.1\t26448\t26450\n", "NC_047559.1\t26463\t26465\n", "NC_047559.1\t26485\t26487\n", "NC_047559.1\t26509\t26511\n", "NC_047559.1\t26532\t26534\n", "NC_047559.1\t26547\t26549\n", "NC_047559.1\t26555\t26557\n", "NC_047559.1\t26561\t26563\n", "\n", "==> zr3644_4_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-TE <==\n", "NC_047559.1\t154507\t154509\n", "NC_047559.1\t335373\t335375\n", "NC_047559.1\t335375\t335377\n", "NC_047559.1\t335399\t335401\n", "NC_047559.1\t335417\t335419\n", "NC_047559.1\t344803\t344805\n", "NC_047559.1\t344829\t344831\n", "NC_047559.1\t344838\t344840\n", "NC_047559.1\t344861\t344863\n", "NC_047559.1\t350807\t350809\n", "\n", "==> zr3644_4_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-TE <==\n", "NC_047559.1\t26419\t26421\n", "NC_047559.1\t26448\t26450\n", "NC_047559.1\t26463\t26465\n", "NC_047559.1\t26485\t26487\n", "NC_047559.1\t26509\t26511\n", "NC_047559.1\t26532\t26534\n", "NC_047559.1\t38166\t38168\n", "NC_047559.1\t41242\t41244\n", "NC_047559.1\t42392\t42394\n", "NC_047559.1\t44374\t44376\n", "\n", "==> zr3644_4_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-TE <==\n", "NC_047559.1\t15746\t15748\n", "NC_047559.1\t24588\t24590\n", "NC_047559.1\t26547\t26549\n", "NC_047559.1\t26555\t26557\n", "NC_047559.1\t26561\t26563\n", "NC_047559.1\t26573\t26575\n", "NC_047559.1\t26591\t26593\n", "NC_047559.1\t26593\t26595\n", "NC_047559.1\t26648\t26650\n", "NC_047559.1\t26651\t26653\n", "\n", "==> zr3644_5_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-TE <==\n", "NC_047559.1\t140539\t140541\n", "NC_047559.1\t140557\t140559\n", "NC_047559.1\t140589\t140591\n", "NC_047559.1\t140640\t140642\n", "NC_047559.1\t141717\t141719\n", "NC_047559.1\t141751\t141753\n", "NC_047559.1\t141777\t141779\n", "NC_047559.1\t141800\t141802\n", "NC_047559.1\t141853\t141855\n", "NC_047559.1\t141939\t141941\n", "\n", "==> zr3644_5_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-TE <==\n", "NC_047559.1\t26419\t26421\n", "NC_047559.1\t26463\t26465\n", "NC_047559.1\t34808\t34810\n", "NC_047559.1\t34835\t34837\n", "NC_047559.1\t46918\t46920\n", "NC_047559.1\t50568\t50570\n", "NC_047559.1\t51037\t51039\n", "NC_047559.1\t51099\t51101\n", "NC_047559.1\t51178\t51180\n", "NC_047559.1\t51180\t51182\n", "\n", "==> zr3644_5_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-TE <==\n", "NC_047559.1\t15746\t15748\n", "NC_047559.1\t26448\t26450\n", "NC_047559.1\t26509\t26511\n", "NC_047559.1\t26532\t26534\n", "NC_047559.1\t26547\t26549\n", "NC_047559.1\t26555\t26557\n", "NC_047559.1\t26561\t26563\n", "NC_047559.1\t26573\t26575\n", "NC_047559.1\t26591\t26593\n", "NC_047559.1\t26593\t26595\n", "\n", "==> zr3644_6_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-TE <==\n", "NC_047559.1\t56231\t56233\n", "NC_047559.1\t139945\t139947\n", "NC_047559.1\t139954\t139956\n", "NC_047559.1\t139972\t139974\n", "NC_047559.1\t139998\t140000\n", "NC_047559.1\t140539\t140541\n", "NC_047559.1\t140557\t140559\n", "NC_047559.1\t140589\t140591\n", "NC_047559.1\t142406\t142408\n", "NC_047559.1\t142411\t142413\n", "\n", "==> zr3644_6_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-TE <==\n", "NC_047559.1\t27132\t27134\n", "NC_047559.1\t33445\t33447\n", "NC_047559.1\t42280\t42282\n", "NC_047559.1\t43952\t43954\n", "NC_047559.1\t51037\t51039\n", "NC_047559.1\t51298\t51300\n", "NC_047559.1\t56029\t56031\n", "NC_047559.1\t56037\t56039\n", "NC_047559.1\t56073\t56075\n", "NC_047559.1\t56090\t56092\n", "\n", "==> zr3644_6_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-TE <==\n", "NC_047559.1\t15746\t15748\n", "NC_047559.1\t26419\t26421\n", "NC_047559.1\t26448\t26450\n", "NC_047559.1\t26463\t26465\n", "NC_047559.1\t26485\t26487\n", "NC_047559.1\t26509\t26511\n", "NC_047559.1\t26532\t26534\n", "NC_047559.1\t26547\t26549\n", "NC_047559.1\t26555\t26557\n", "NC_047559.1\t26561\t26563\n", "\n", "==> zr3644_7_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-TE <==\n", "NC_047559.1\t56231\t56233\n", "NC_047559.1\t140589\t140591\n", "NC_047559.1\t140640\t140642\n", "NC_047559.1\t141777\t141779\n", "NC_047559.1\t141800\t141802\n", "NC_047559.1\t141868\t141870\n", "NC_047559.1\t141888\t141890\n", "NC_047559.1\t141905\t141907\n", "NC_047559.1\t142357\t142359\n", "NC_047559.1\t142371\t142373\n", "\n", "==> zr3644_7_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-TE <==\n", "NC_047559.1\t26770\t26772\n", "NC_047559.1\t32017\t32019\n", "NC_047559.1\t43420\t43422\n", "NC_047559.1\t44234\t44236\n", "NC_047559.1\t45010\t45012\n", "NC_047559.1\t49963\t49965\n", "NC_047559.1\t51249\t51251\n", "NC_047559.1\t51317\t51319\n", "NC_047559.1\t51319\t51321\n", "NC_047559.1\t55915\t55917\n", "\n", "==> zr3644_7_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-TE <==\n", "NC_047559.1\t15746\t15748\n", "NC_047559.1\t26419\t26421\n", "NC_047559.1\t26448\t26450\n", "NC_047559.1\t26463\t26465\n", "NC_047559.1\t26485\t26487\n", "NC_047559.1\t26509\t26511\n", "NC_047559.1\t26532\t26534\n", "NC_047559.1\t26547\t26549\n", "NC_047559.1\t26555\t26557\n", "NC_047559.1\t26561\t26563\n", "\n", "==> zr3644_8_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-TE <==\n", "NC_047559.1\t26677\t26679\n", "NC_047559.1\t344785\t344787\n", "NC_047559.1\t344794\t344796\n", "NC_047559.1\t344803\t344805\n", "NC_047559.1\t344812\t344814\n", "NC_047559.1\t344829\t344831\n", "NC_047559.1\t344838\t344840\n", "NC_047559.1\t378417\t378419\n", "NC_047559.1\t378455\t378457\n", "NC_047559.1\t425255\t425257\n", "\n", "==> zr3644_8_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-TE <==\n", "NC_047559.1\t26699\t26701\n", "NC_047559.1\t38166\t38168\n", "NC_047559.1\t43077\t43079\n", "NC_047559.1\t43952\t43954\n", "NC_047559.1\t49455\t49457\n", "NC_047559.1\t49823\t49825\n", "NC_047559.1\t51178\t51180\n", "NC_047559.1\t51180\t51182\n", "NC_047559.1\t51213\t51215\n", "NC_047559.1\t53350\t53352\n", "\n", "==> zr3644_8_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-TE <==\n", "NC_047559.1\t15746\t15748\n", "NC_047559.1\t26419\t26421\n", "NC_047559.1\t26448\t26450\n", "NC_047559.1\t26463\t26465\n", "NC_047559.1\t26485\t26487\n", "NC_047559.1\t26509\t26511\n", "NC_047559.1\t26532\t26534\n", "NC_047559.1\t26547\t26549\n", "NC_047559.1\t26555\t26557\n", "NC_047559.1\t26561\t26563\n", "\n", "==> zr3644_9_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-TE <==\n", "NC_047559.1\t44918\t44920\n", "NC_047559.1\t140520\t140522\n", "NC_047559.1\t140539\t140541\n", "NC_047559.1\t140557\t140559\n", "NC_047559.1\t140589\t140591\n", "NC_047559.1\t140640\t140642\n", "NC_047559.1\t141751\t141753\n", "NC_047559.1\t141777\t141779\n", "NC_047559.1\t141800\t141802\n", "NC_047559.1\t142406\t142408\n", "\n", "==> zr3644_9_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-TE <==\n", "NC_047559.1\t35403\t35405\n", "NC_047559.1\t35473\t35475\n", "NC_047559.1\t42709\t42711\n", "NC_047559.1\t45010\t45012\n", "NC_047559.1\t45033\t45035\n", "NC_047559.1\t46646\t46648\n", "NC_047559.1\t46678\t46680\n", "NC_047559.1\t52962\t52964\n", "NC_047559.1\t56073\t56075\n", "NC_047559.1\t56082\t56084\n", "\n", "==> zr3644_9_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-TE <==\n", "NC_047559.1\t15746\t15748\n", "NC_047559.1\t26419\t26421\n", "NC_047559.1\t26448\t26450\n", "NC_047559.1\t26463\t26465\n", "NC_047559.1\t26485\t26487\n", "NC_047559.1\t26509\t26511\n", "NC_047559.1\t26532\t26534\n", "NC_047559.1\t26547\t26549\n", "NC_047559.1\t26555\t26557\n", "NC_047559.1\t26561\t26563\n", "\n", "==> zr3644_union-averages_5x.bedgraph-Meth.bed-TE <==\n", "NC_047559.1\t60313\t60315\n", "NC_047559.1\t60371\t60373\n", "NC_047559.1\t139898\t139900\n", "NC_047559.1\t139912\t139914\n", "NC_047559.1\t139926\t139928\n", "NC_047559.1\t139945\t139947\n", "NC_047559.1\t139954\t139956\n", "NC_047559.1\t139972\t139974\n", "NC_047559.1\t140539\t140541\n", "NC_047559.1\t141853\t141855\n", "\n", "==> zr3644_union-averages_5x.bedgraph-sparseMeth.bed-TE <==\n", "NC_047559.1\t26699\t26701\n", "NC_047559.1\t44918\t44920\n", "NC_047559.1\t46646\t46648\n", "NC_047559.1\t46678\t46680\n", "NC_047559.1\t47777\t47779\n", "NC_047559.1\t47794\t47796\n", "NC_047559.1\t52962\t52964\n", "NC_047559.1\t56037\t56039\n", "NC_047559.1\t56073\t56075\n", "NC_047559.1\t56090\t56092\n", "\n", "==> zr3644_union-averages_5x.bedgraph-unMeth.bed-TE <==\n", "NC_047559.1\t15746\t15748\n", "NC_047559.1\t24588\t24590\n", "NC_047559.1\t25485\t25487\n", "NC_047559.1\t25667\t25669\n", "NC_047559.1\t26135\t26137\n", "NC_047559.1\t26419\t26421\n", "NC_047559.1\t26448\t26450\n", "NC_047559.1\t26463\t26465\n", "NC_047559.1\t26485\t26487\n", "NC_047559.1\t26509\t26511\n" ] } ], "source": [ "#Check output\n", "!head *TE" ] }, { "cell_type": "code", "execution_count": 73, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ " 189566 zr3644_10_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-TE\n", " 251548 zr3644_10_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-TE\n", " 1637275 zr3644_10_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-TE\n", " 198940 zr3644_11_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-TE\n", " 266854 zr3644_11_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-TE\n", " 1744645 zr3644_11_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-TE\n", " 169747 zr3644_12_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-TE\n", " 227639 zr3644_12_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-TE\n", " 1583872 zr3644_12_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-TE\n", " 191696 zr3644_13_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-TE\n", " 258316 zr3644_13_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-TE\n", " 1704139 zr3644_13_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-TE\n", " 150122 zr3644_14_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-TE\n", " 167061 zr3644_14_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-TE\n", " 1240157 zr3644_14_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-TE\n", " 212528 zr3644_15_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-TE\n", " 265705 zr3644_15_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-TE\n", " 1805639 zr3644_15_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-TE\n", " 172359 zr3644_16_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-TE\n", " 231415 zr3644_16_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-TE\n", " 1534846 zr3644_16_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-TE\n", " 188433 zr3644_17_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-TE\n", " 234234 zr3644_17_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-TE\n", " 1706444 zr3644_17_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-TE\n", " 180080 zr3644_18_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-TE\n", " 243643 zr3644_18_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-TE\n", " 1578303 zr3644_18_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-TE\n", " 169985 zr3644_19_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-TE\n", " 231971 zr3644_19_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-TE\n", " 1586257 zr3644_19_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-TE\n", " 155842 zr3644_1_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-TE\n", " 222174 zr3644_1_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-TE\n", " 1554468 zr3644_1_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-TE\n", " 186520 zr3644_20_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-TE\n", " 253945 zr3644_20_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-TE\n", " 1686914 zr3644_20_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-TE\n", " 185749 zr3644_21_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-TE\n", " 248896 zr3644_21_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-TE\n", " 1648072 zr3644_21_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-TE\n", " 167106 zr3644_22_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-TE\n", " 227297 zr3644_22_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-TE\n", " 1514641 zr3644_22_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-TE\n", " 143674 zr3644_23_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-TE\n", " 197405 zr3644_23_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-TE\n", " 1321271 zr3644_23_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-TE\n", " 181355 zr3644_24_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-TE\n", " 241127 zr3644_24_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-TE\n", " 1645846 zr3644_24_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-TE\n", " 191988 zr3644_2_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-TE\n", " 232566 zr3644_2_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-TE\n", " 1733705 zr3644_2_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-TE\n", " 148464 zr3644_3_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-TE\n", " 204353 zr3644_3_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-TE\n", " 1336699 zr3644_3_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-TE\n", " 173201 zr3644_4_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-TE\n", " 239368 zr3644_4_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-TE\n", " 1624451 zr3644_4_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-TE\n", " 165487 zr3644_5_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-TE\n", " 223615 zr3644_5_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-TE\n", " 1473955 zr3644_5_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-TE\n", " 186435 zr3644_6_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-TE\n", " 250182 zr3644_6_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-TE\n", " 1670034 zr3644_6_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-TE\n", " 241445 zr3644_7_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-TE\n", " 331203 zr3644_7_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-TE\n", " 2207082 zr3644_7_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-TE\n", " 160502 zr3644_8_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-TE\n", " 215954 zr3644_8_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-TE\n", " 1417725 zr3644_8_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-TE\n", " 167985 zr3644_9_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-TE\n", " 232000 zr3644_9_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-TE\n", " 1464137 zr3644_9_R1_val_1_val_1_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-TE\n", " 295204 zr3644_union-averages_5x.bedgraph-Meth.bed-TE\n", " 445759 zr3644_union-averages_5x.bedgraph-sparseMeth.bed-TE\n", " 3255637 zr3644_union-averages_5x.bedgraph-unMeth.bed-TE\n", " 52394857 total\n" ] } ], "source": [ "#Count number of overlaps\n", "!wc -l *TE" ] }, { "cell_type": "code", "execution_count": 74, "metadata": { "collapsed": true }, "outputs": [], "source": [ "#Get line counts for each fine\n", "# Remove 28th line (total entries)\n", "#Ensure output is tab-delimited\n", "#Save output\n", "!wc -l *-TE \\\n", "| sed '76,$ d' \\\n", "| awk '{print $1\"\\t\"$2}' \\\n", "> zr3644_5x-TE-counts.txt" ] }, { "cell_type": "code", "execution_count": null, "metadata": { "collapsed": true }, "outputs": [], "source": [] } ], "metadata": { "anaconda-cloud": {}, "kernelspec": { "display_name": "Python [default]", "language": "python", "name": "python3" }, "language_info": { "codemirror_mode": { "name": "ipython", "version": 3 }, "file_extension": ".py", "mimetype": "text/x-python", "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", "version": "3.5.2" } }, "nbformat": 4, "nbformat_minor": 1 }