{ "cells": [ { "cell_type": "markdown", "metadata": {}, "source": [ "# Characterizing CpG Methylation (5x data)\n", "\n", "In this notebook, general methylation landscapes in *Montipora capitata* and *Pocillopora acuta* will be characterized based on WGSB, RRBS, and MBD-BSseq data. I will also assess CG motif overlaps with various genome feature tracks to understand where methylation may occur across the genome. I will use 5x data.\n", "\n", "1. Characterize overlap between CG motifs and genome feature tracks\n", "1. Download coverage files\n", "2. Characterize methylation for each CpG dinucleotide\n", "3. Characterize genomic locations of all sequenced data, methylated CpGs, sparsely methylated CpGs, and unmethylated CpGs for each sequencing type" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "## 0. Set working directory and obtain checksums" ] }, { "cell_type": "code", "execution_count": 1, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "/Users/yaamini/Documents/Meth_Compare/scripts\r\n" ] } ], "source": [ "!pwd" ] }, { "cell_type": "code", "execution_count": 2, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "/Users/yaamini/Documents/Meth_Compare/analyses\n" ] } ], "source": [ "cd ../analyses/" ] }, { "cell_type": "code", "execution_count": 3, "metadata": { "collapsed": true }, "outputs": [], "source": [ "#!mkdir Characterizing-CpG-Methylation-5x" ] }, { "cell_type": "code", "execution_count": 4, "metadata": { "collapsed": false, "scrolled": true }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "/Users/yaamini/Documents/Meth_Compare/analyses/Characterizing-CpG-Methylation-5x\n" ] } ], "source": [ "cd Characterizing-CpG-Methylation-5x/" ] }, { "cell_type": "code", "execution_count": 5, "metadata": { "collapsed": false, "scrolled": true }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "--2020-07-09 09:45:04-- https://gannet.fish.washington.edu/metacarcinus/FROGER_meth_compare/20200410/all_031520-TG-bs_files_GANNET_md5sum.txt\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", "HTTP request sent, awaiting response... 200 OK\n", "Length: 90413 (88K) [text/plain]\n", "Saving to: ‘all_031520-TG-bs_files_GANNET_md5sum.txt.1’\n", "\n", "all_031520-TG-bs_fi 100%[===================>] 88.29K --.-KB/s in 0.001s \n", "\n", "2020-07-09 09:45:04 (63.7 MB/s) - ‘all_031520-TG-bs_files_GANNET_md5sum.txt.1’ saved [90413/90413]\n", "\n" ] } ], "source": [ "!wget https://gannet.fish.washington.edu/metacarcinus/FROGER_meth_compare/20200410/all_031520-TG-bs_files_GANNET_md5sum.txt" ] }, { "cell_type": "code", "execution_count": 6, "metadata": { "collapsed": false, "scrolled": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "04829778554df5986ae415fcda3b7e81 /Volumes/web/seashell/bu-mox/scrubbed/031520-TG-bs/Meth9_R1_001_val_1.fq.gz\r\n", "e1048fea898bc32cb03ff801534183d9 /Volumes/web/seashell/bu-mox/scrubbed/031520-TG-bs/Meth15_R2_001_val_2.fq.gz\r\n", "d6e026bb59b10a11ad9b51b8acdd18a7 /Volumes/web/seashell/bu-mox/scrubbed/031520-TG-bs/Meth5_R2_001_val_2.fq.gz\r\n", "bfe70cae27f3251ead4e6686391940ca /Volumes/web/seashell/bu-mox/scrubbed/031520-TG-bs/Meth8_R1_001_val_1.fq.gz_G_to_A.fastq\r\n", "26c6f90dd9cef5e30f32e312007f3176 /Volumes/web/seashell/bu-mox/scrubbed/031520-TG-bs/Meth15_R2_001_val_2.fq.gz_G_to_A.fastq\r\n", "f41790ce58777f20ee742cba75692065 /Volumes/web/seashell/bu-mox/scrubbed/031520-TG-bs/Meth1_R1_001_val_1.fq.gz\r\n", "4ed014c23ba4c28681d5b4af17e95346 /Volumes/web/seashell/bu-mox/scrubbed/031520-TG-bs/Meth14_R1_001_val_1.fq.gz\r\n", "fc3ad5f9624c63e28bab515b5848158c /Volumes/web/seashell/bu-mox/scrubbed/031520-TG-bs/Meth13_R2_001_val_2.fq.gz_C_to_T.fastq\r\n", "8b2c14989c4638fa2cdd7d16a36a7b99 /Volumes/web/seashell/bu-mox/scrubbed/031520-TG-bs/Pact_tg/Meth6_R1_001_val_1_bismark_bt2_PE_report.txt\r\n", "edeeb18d68c753dfb2a0cd197123d847 /Volumes/web/seashell/bu-mox/scrubbed/031520-TG-bs/Pact_tg/Meth6_R1_001_val_1_bismark_bt2_pe.bam\r\n" ] } ], "source": [ "!head all_031520-TG-bs_files_GANNET_md5sum.txt" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "### *M. capitata*" ] }, { "cell_type": "code", "execution_count": 7, "metadata": { "collapsed": true }, "outputs": [], "source": [ "#Get all lines from original checksum document\n", "#Extract information for 5x bedgraphs\n", "#Extract information for Mcap data only\n", "#Only keep the first 32 characters in each line (md5sum hashes)\n", "#Save hashes\n", "!cat all_031520-TG-bs_files_GANNET_md5sum.txt \\\n", "| grep 5x.bedgraph \\\n", "| grep Mcap \\\n", "| cut -c1-32 \\\n", "> Mcap-5xbedgraph-GANNET-md5sum-hashes.txt" ] }, { "cell_type": "code", "execution_count": 8, "metadata": { "collapsed": true }, "outputs": [], "source": [ "#Get all lines from original checksum document\n", "#Extract information for 5x bedgraphs\n", "#Extract information for Mcap data only\n", "#Reverse order of characters in each line\n", "#Only keep the first 48 characters in each line\n", "#actually the last 48 characters in the original file, which maps to paths locally\n", "#Reverse characters\n", "#Save paths\n", "!cat all_031520-TG-bs_files_GANNET_md5sum.txt \\\n", "| grep 5x.bedgraph \\\n", "| grep Mcap \\\n", "| rev \\\n", "| cut -c1-47 \\\n", "| rev \\\n", "> Mcap-5xbedgraph-GANNET-md5sum-paths.txt" ] }, { "cell_type": "code", "execution_count": 9, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "04fb72d5df60656e6cec15637164fbec\tMeth16_R1_001_val_1_bismark_bt2_pe._5x.bedgraph\n", "b2f097299df0cb7d518d22338fdcf39f\tMeth12_R1_001_val_1_bismark_bt2_pe._5x.bedgraph\n", "073d1c40116a3f93f7a7022cfb4cd3d2\tMeth17_R1_001_val_1_bismark_bt2_pe._5x.bedgraph\n", "83035e7e47b8ad486de22dacc17ae8ed\tMeth10_R1_001_val_1_bismark_bt2_pe._5x.bedgraph\n", "a255210553db073e5458ccb523a34798\tMeth18_R1_001_val_1_bismark_bt2_pe._5x.bedgraph\n", "6493359aad0b4228f65b5e563d337ceb\tMeth11_R1_001_val_1_bismark_bt2_pe._5x.bedgraph\n", "fc0f66cf04ffebe76d61c1db75cfed6e\tMeth14_R1_001_val_1_bismark_bt2_pe._5x.bedgraph\n", "1d7c24b238dc72cd92346213b3523611\tMeth15_R1_001_val_1_bismark_bt2_pe._5x.bedgraph\n", "2bb476cb98072f0e76bfb5c318246c38\tMeth13_R1_001_val_1_bismark_bt2_pe._5x.bedgraph\n", " 9 Mcap-5xbedgraph-GANNET-md5sum.txt\n" ] } ], "source": [ "#Paste hashes and paths to create a md5sum file\n", "#Save checksum file\n", "#Check output\n", "#Count number of lines \n", "!paste Mcap-5xbedgraph-GANNET-md5sum-hashes.txt Mcap-5xbedgraph-GANNET-md5sum-paths.txt \\\n", "> Mcap-5xbedgraph-GANNET-md5sum.txt\n", "!head Mcap-5xbedgraph-GANNET-md5sum.txt\n", "!wc -l Mcap-5xbedgraph-GANNET-md5sum.txt" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "### *P. acuta*" ] }, { "cell_type": "code", "execution_count": 10, "metadata": { "collapsed": true }, "outputs": [], "source": [ "#Get all lines from original checksum document\n", "#Extract information for 5x bedgraphs\n", "#Extract information for Pact data only\n", "#Only keep the first 32 characters in each line (md5sum hashes)\n", "#Save hashes\n", "!cat all_031520-TG-bs_files_GANNET_md5sum.txt \\\n", "| grep 5x.bedgraph \\\n", "| grep Pact \\\n", "| cut -c1-32 \\\n", "> Pact-5xbedgraph-GANNET-md5sum-hashes.txt" ] }, { "cell_type": "code", "execution_count": 11, "metadata": { "collapsed": true }, "outputs": [], "source": [ "#Get all lines from original checksum document\n", "#Extract information for 5x bedgraphs\n", "#Extract information for Pact data only\n", "#Reverse order of characters in each line\n", "#Only keep the first 48 characters in each line\n", "#actually the last 48 characters in the original file, which maps to paths locally\n", "#Reverse characters\n", "#Save paths\n", "!cat all_031520-TG-bs_files_GANNET_md5sum.txt \\\n", "| grep 5x.bedgraph \\\n", "| grep Pact \\\n", "| rev \\\n", "| cut -c1-46 \\\n", "| rev \\\n", "> Pact-5xbedgraph-GANNET-md5sum-paths.txt" ] }, { "cell_type": "code", "execution_count": 12, "metadata": { "collapsed": false, "scrolled": true }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "c838562956c7abe3656a2b7438a40dc1\tMeth8_R1_001_val_1_bismark_bt2_pe._5x.bedgraph\n", "c9a4b002113e2501d81e4762cf952b79\tMeth9_R1_001_val_1_bismark_bt2_pe._5x.bedgraph\n", "1ec934f5b4ce012b64b77dd69d70ee5f\tMeth2_R1_001_val_1_bismark_bt2_pe._5x.bedgraph\n", "c456156b7f6a11543d8dc697e8e74b4e\tMeth3_R1_001_val_1_bismark_bt2_pe._5x.bedgraph\n", "d634ffc3f062d248e36b8dddc9a315e0\tMeth1_R1_001_val_1_bismark_bt2_pe._5x.bedgraph\n", "a2b842c439c3df3fb699690cd5b55d5a\tMeth7_R1_001_val_1_bismark_bt2_pe._5x.bedgraph\n", "5994ba73d412d8992f2465b148f5ae80\tMeth6_R1_001_val_1_bismark_bt2_pe._5x.bedgraph\n", "ed4428a6c8cb6a4964687d91c0d8ccb3\tMeth5_R1_001_val_1_bismark_bt2_pe._5x.bedgraph\n", "736fd3802ce1b45b6eb32abf6e1bcb3f\tMeth4_R1_001_val_1_bismark_bt2_pe._5x.bedgraph\n", " 9 Pact-5xbedgraph-GANNET-md5sum.txt\n" ] } ], "source": [ "#Paste hashes and paths to create a md5sum file\n", "#Save checksum file\n", "#Check output\n", "#Count number of lines \n", "!paste Pact-5xbedgraph-GANNET-md5sum-hashes.txt Pact-5xbedgraph-GANNET-md5sum-paths.txt \\\n", "> Pact-5xbedgraph-GANNET-md5sum.txt\n", "!head Pact-5xbedgraph-GANNET-md5sum.txt\n", "!wc -l Pact-5xbedgraph-GANNET-md5sum.txt" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "## *M. capitata*" ] }, { "cell_type": "code", "execution_count": 13, "metadata": { "collapsed": true }, "outputs": [], "source": [ "#Make a directory for Mcap output\n", "#!mkdir Mcap" ] }, { "cell_type": "code", "execution_count": 14, "metadata": { "collapsed": false, "scrolled": true }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "/Users/yaamini/Documents/Meth_Compare/analyses/Characterizing-CpG-Methylation-5x/Mcap\n" ] } ], "source": [ "cd Mcap/" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "### 1. Characterize CG motif locations in feature tracks" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "#### 1a. Set variable paths" ] }, { "cell_type": "code", "execution_count": 15, "metadata": { "collapsed": true }, "outputs": [], "source": [ "bedtoolsDirectory = \"/usr/local/bin/\"" ] }, { "cell_type": "code", "execution_count": 16, "metadata": { "collapsed": true }, "outputs": [], "source": [ "mcGenes = \"../../../genome-feature-files/Mcap.GFFannotation.gene.gff\"" ] }, { "cell_type": "code", "execution_count": 17, "metadata": { "collapsed": true }, "outputs": [], "source": [ "mcCDS = \"../../../genome-feature-files/Mcap.GFFannotation.CDS.gff\"" ] }, { "cell_type": "code", "execution_count": 18, "metadata": { "collapsed": true }, "outputs": [], "source": [ "mcIntron = \"../../../genome-feature-files/Mcap.GFFannotation.intron.gff\"" ] }, { "cell_type": "code", "execution_count": 19, "metadata": { "collapsed": true }, "outputs": [], "source": [ "mcFlanks = \"../../../genome-feature-files/Mcap.GFFannotation.flanks.gff\"" ] }, { "cell_type": "code", "execution_count": 20, "metadata": { "collapsed": true }, "outputs": [], "source": [ "mcUpstream = \"../../../genome-feature-files/Mcap.GFFannotation.flanks.Upstream.gff\"" ] }, { "cell_type": "code", "execution_count": 21, "metadata": { "collapsed": true }, "outputs": [], "source": [ "mcDownstream = \"../../../genome-feature-files/Mcap.GFFannotation.flanks.Downstream.gff\"" ] }, { "cell_type": "code", "execution_count": 22, "metadata": { "collapsed": true }, "outputs": [], "source": [ "mcIntergenic = \"../../../genome-feature-files/Mcap.GFFannotation.intergenic.bed\"" ] }, { "cell_type": "code", "execution_count": 23, "metadata": { "collapsed": true }, "outputs": [], "source": [ "mcCGMotifs = \"../../../genome-feature-files/Mcap_CpG.gff\"" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "#### 1b. Check variable paths" ] }, { "cell_type": "code", "execution_count": 24, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "1\tAUGUSTUS\tgene\t18387\t18755\t0.97\t-\t.\tg21532\n", "1\tAUGUSTUS\tgene\t22321\t27293\t0.23\t-\t.\tg21533\n", "1\tAUGUSTUS\tgene\t37447\t52266\t1\t+\t.\tg21534\n", "1\tAUGUSTUS\tgene\t58322\t62557\t1\t-\t.\tg21535\n", "1\tAUGUSTUS\tgene\t64466\t84798\t1\t+\t.\tg21536\n", "1\tAUGUSTUS\tgene\t88347\t97184\t1\t+\t.\tg21537\n", "1\tAUGUSTUS\tgene\t100215\t109729\t0.99\t-\t.\tg21538\n", "1\tAUGUSTUS\tgene\t109867\t128510\t0.89\t+\t.\tg21539\n", "1\tAUGUSTUS\tgene\t132854\t139285\t1\t-\t.\tg21540\n", "1\tAUGUSTUS\tgene\t148344\t149588\t0.44\t+\t.\tg21541\n", " 63227 ../../../genome-feature-files/Mcap.GFFannotation.gene.gff\n" ] } ], "source": [ "!head {mcGenes}\n", "!wc -l {mcGenes}" ] }, { "cell_type": "code", "execution_count": 25, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "1\tAUGUSTUS\tCDS\t18387\t18755\t0.97\t-\t0\ttranscript_id \"g21532.t1\"; gene_id \"g21532\";\n", "1\tAUGUSTUS\tCDS\t22321\t22608\t0.55\t-\t0\ttranscript_id \"g21533.t1\"; gene_id \"g21533\";\n", "1\tAUGUSTUS\tCDS\t26301\t27293\t0.29\t-\t0\ttranscript_id \"g21533.t1\"; gene_id \"g21533\";\n", "1\tAUGUSTUS\tCDS\t37447\t37810\t1\t+\t0\ttranscript_id \"g21534.t1\"; gene_id \"g21534\";\n", "1\tAUGUSTUS\tCDS\t45038\t45208\t1\t+\t2\ttranscript_id \"g21534.t1\"; gene_id \"g21534\";\n", "1\tAUGUSTUS\tCDS\t46625\t47272\t1\t+\t2\ttranscript_id \"g21534.t1\"; gene_id \"g21534\";\n", "1\tAUGUSTUS\tCDS\t49943\t50132\t1\t+\t2\ttranscript_id \"g21534.t1\"; gene_id \"g21534\";\n", "1\tAUGUSTUS\tCDS\t51903\t52266\t1\t+\t1\ttranscript_id \"g21534.t1\"; gene_id \"g21534\";\n", "1\tAUGUSTUS\tCDS\t58322\t59506\t1\t-\t0\ttranscript_id \"g21535.t1\"; gene_id \"g21535\";\n", "1\tAUGUSTUS\tCDS\t62261\t62557\t1\t-\t0\ttranscript_id \"g21535.t1\"; gene_id \"g21535\";\n", " 283926 ../../../genome-feature-files/Mcap.GFFannotation.CDS.gff\n" ] } ], "source": [ "!head {mcCDS}\n", "!wc -l {mcCDS}" ] }, { "cell_type": "code", "execution_count": 26, "metadata": { "collapsed": false, "scrolled": true }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "1\tAUGUSTUS\tintron\t22609\t26300\t0.25\t-\t.\ttranscript_id \"g21533.t1\"; gene_id \"g21533\";\n", "1\tAUGUSTUS\tintron\t37811\t45037\t1\t+\t.\ttranscript_id \"g21534.t1\"; gene_id \"g21534\";\n", "1\tAUGUSTUS\tintron\t45209\t46624\t1\t+\t.\ttranscript_id \"g21534.t1\"; gene_id \"g21534\";\n", "1\tAUGUSTUS\tintron\t47273\t49942\t1\t+\t.\ttranscript_id \"g21534.t1\"; gene_id \"g21534\";\n", "1\tAUGUSTUS\tintron\t50133\t51902\t1\t+\t.\ttranscript_id \"g21534.t1\"; gene_id \"g21534\";\n", "1\tAUGUSTUS\tintron\t59507\t62260\t1\t-\t.\ttranscript_id \"g21535.t1\"; gene_id \"g21535\";\n", "1\tAUGUSTUS\tintron\t64578\t64654\t1\t+\t.\ttranscript_id \"g21536.t1\"; gene_id \"g21536\";\n", "1\tAUGUSTUS\tintron\t64735\t67263\t1\t+\t.\ttranscript_id \"g21536.t1\"; gene_id \"g21536\";\n", "1\tAUGUSTUS\tintron\t67319\t71345\t1\t+\t.\ttranscript_id \"g21536.t1\"; gene_id \"g21536\";\n", "1\tAUGUSTUS\tintron\t71456\t72865\t1\t+\t.\ttranscript_id \"g21536.t1\"; gene_id \"g21536\";\n", " 221428 ../../../genome-feature-files/Mcap.GFFannotation.intron.gff\n" ] } ], "source": [ "!head {mcIntron}\n", "!wc -l {mcIntron}" ] }, { "cell_type": "code", "execution_count": 27, "metadata": { "collapsed": false, "scrolled": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "1\tAUGUSTUS\tgene\t17387\t18386\t0.97\t-\t.\tg21532\n", "1\tAUGUSTUS\tgene\t18756\t19755\t0.97\t-\t.\tg21532\n", "1\tAUGUSTUS\tgene\t21321\t22320\t0.23\t-\t.\tg21533\n", "1\tAUGUSTUS\tgene\t27294\t28293\t0.23\t-\t.\tg21533\n", "1\tAUGUSTUS\tgene\t36447\t37446\t1\t+\t.\tg21534\n", "1\tAUGUSTUS\tgene\t52267\t53266\t1\t+\t.\tg21534\n", "1\tAUGUSTUS\tgene\t57322\t58321\t1\t-\t.\tg21535\n", "1\tAUGUSTUS\tgene\t62558\t63557\t1\t-\t.\tg21535\n", "1\tAUGUSTUS\tgene\t63466\t64465\t1\t+\t.\tg21536\n", "1\tAUGUSTUS\tgene\t84799\t85798\t1\t+\t.\tg21536\n", " 133644 ../../../genome-feature-files/Mcap.GFFannotation.flanks.gff\n" ] } ], "source": [ "!head {mcFlanks}\n", "!wc -l {mcFlanks}" ] }, { "cell_type": "code", "execution_count": 28, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "1\tAUGUSTUS\tgene\t18756\t19755\t0.97\t-\t.\tg21532\n", "1\tAUGUSTUS\tgene\t27294\t28293\t0.23\t-\t.\tg21533\n", "1\tAUGUSTUS\tgene\t36447\t37446\t1\t+\t.\tg21534\n", "1\tAUGUSTUS\tgene\t62558\t63557\t1\t-\t.\tg21535\n", "1\tAUGUSTUS\tgene\t63466\t64465\t1\t+\t.\tg21536\n", "1\tAUGUSTUS\tgene\t87347\t88346\t1\t+\t.\tg21537\n", "1\tAUGUSTUS\tgene\t109730\t109866\t0.99\t-\t.\tg21538\n", "1\tAUGUSTUS\tgene\t109730\t109866\t0.89\t+\t.\tg21539\n", "1\tAUGUSTUS\tgene\t139286\t140285\t1\t-\t.\tg21540\n", "1\tAUGUSTUS\tgene\t147344\t148343\t0.44\t+\t.\tg21541\n", " 66969 ../../../genome-feature-files/Mcap.GFFannotation.flanks.Upstream.gff\n" ] } ], "source": [ "!head {mcUpstream}\n", "!wc -l {mcUpstream}" ] }, { "cell_type": "code", "execution_count": 29, "metadata": { "collapsed": false, "scrolled": true }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "1\tAUGUSTUS\tgene\t17387\t18386\t0.97\t-\t.\tg21532\n", "1\tAUGUSTUS\tgene\t21321\t22320\t0.23\t-\t.\tg21533\n", "1\tAUGUSTUS\tgene\t52267\t53266\t1\t+\t.\tg21534\n", "1\tAUGUSTUS\tgene\t57322\t58321\t1\t-\t.\tg21535\n", "1\tAUGUSTUS\tgene\t84799\t85798\t1\t+\t.\tg21536\n", "1\tAUGUSTUS\tgene\t97185\t98184\t1\t+\t.\tg21537\n", "1\tAUGUSTUS\tgene\t99215\t100214\t0.99\t-\t.\tg21538\n", "1\tAUGUSTUS\tgene\t128511\t129510\t0.89\t+\t.\tg21539\n", "1\tAUGUSTUS\tgene\t131854\t132853\t1\t-\t.\tg21540\n", "1\tAUGUSTUS\tgene\t149589\t150588\t0.44\t+\t.\tg21541\n", " 67015 ../../../genome-feature-files/Mcap.GFFannotation.flanks.Downstream.gff\n" ] } ], "source": [ "!head {mcDownstream}\n", "!wc -l {mcDownstream}" ] }, { "cell_type": "code", "execution_count": 30, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "1\t0\t17386\n", "1\t19755\t21320\n", "1\t28293\t36446\n", "1\t53266\t57321\n", "1\t85798\t87346\n", "1\t98184\t99214\n", "1\t129510\t131853\n", "1\t140285\t147343\n", "1\t150588\t155443\n", "1\t158268\t171840\n", " 43853 ../../../genome-feature-files/Mcap.GFFannotation.intergenic.bed\n" ] } ], "source": [ "!head {mcIntergenic}\n", "!wc -l {mcIntergenic}" ] }, { "cell_type": "code", "execution_count": 31, "metadata": { "collapsed": false, "scrolled": true }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "##gff-version 2.0\n", "##date 2020-03-29\n", "##Type DNA 1\n", "1\tfuzznuc\tmisc_feature\t37\t38\t2.000\t+\t.\tSequence \"1.1\" ; note \"*pat pattern1\"\n", "1\tfuzznuc\tmisc_feature\t90\t91\t2.000\t+\t.\tSequence \"1.2\" ; note \"*pat pattern1\"\n", "1\tfuzznuc\tmisc_feature\t121\t122\t2.000\t+\t.\tSequence \"1.3\" ; note \"*pat pattern1\"\n", "1\tfuzznuc\tmisc_feature\t132\t133\t2.000\t+\t.\tSequence \"1.4\" ; note \"*pat pattern1\"\n", "1\tfuzznuc\tmisc_feature\t153\t154\t2.000\t+\t.\tSequence \"1.5\" ; note \"*pat pattern1\"\n", "1\tfuzznuc\tmisc_feature\t170\t171\t2.000\t+\t.\tSequence \"1.6\" ; note \"*pat pattern1\"\n", "1\tfuzznuc\tmisc_feature\t220\t221\t2.000\t+\t.\tSequence \"1.7\" ; note \"*pat pattern1\"\n", " 28684519 ../../../genome-feature-files/Mcap_CpG.gff\n" ] } ], "source": [ "!head {mcCGMotifs}\n", "!wc -l {mcCGMotifs}" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "#### 1c. Characterize overlaps with `bedtools`" ] }, { "cell_type": "code", "execution_count": 32, "metadata": { "collapsed": false, "scrolled": true }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "\r\n", "Tool: bedtools intersect (aka intersectBed)\r\n", "Version: v2.17.0\r\n", "Summary: Report overlaps between two feature files.\r\n", "\r\n", "Usage: bedtools intersect [OPTIONS] -a -b \r\n", "\r\n", "Options: \r\n", "\t-abam\tThe A input file is in BAM format. Output will be BAM as well.\r\n", "\r\n", "\t-ubam\tWrite uncompressed BAM output. Default writes compressed BAM.\r\n", "\r\n", "\t-bed\tWhen using BAM input (-abam), write output as BED. The default\r\n", "\t\tis to write output in BAM when using -abam.\r\n", "\r\n", "\t-wa\tWrite the original entry in A for each overlap.\r\n", "\r\n", "\t-wb\tWrite the original entry in B for each overlap.\r\n", "\t\t- Useful for knowing _what_ A overlaps. Restricted by -f and -r.\r\n", "\r\n", "\t-loj\tPerform a \"left outer join\". That is, for each feature in A\r\n", "\t\treport each overlap with B. If no overlaps are found, \r\n", "\t\treport a NULL feature for B.\r\n", "\r\n", "\t-wo\tWrite the original A and B entries plus the number of base\r\n", "\t\tpairs of overlap between the two features.\r\n", "\t\t- Overlaps restricted by -f and -r.\r\n", "\t\t Only A features with overlap are reported.\r\n", "\r\n", "\t-wao\tWrite the original A and B entries plus the number of base\r\n", "\t\tpairs of overlap between the two features.\r\n", "\t\t- Overlapping features restricted by -f and -r.\r\n", "\t\t However, A features w/o overlap are also reported\r\n", "\t\t with a NULL B feature and overlap = 0.\r\n", "\r\n", "\t-u\tWrite the original A entry _once_ if _any_ overlaps found in B.\r\n", "\t\t- In other words, just report the fact >=1 hit was found.\r\n", "\t\t- Overlaps restricted by -f and -r.\r\n", "\r\n", "\t-c\tFor each entry in A, report the number of overlaps with B.\r\n", "\t\t- Reports 0 for A entries that have no overlap with B.\r\n", "\t\t- Overlaps restricted by -f and -r.\r\n", "\r\n", "\t-v\tOnly report those entries in A that have _no overlaps_ with B.\r\n", "\t\t- Similar to \"grep -v\" (an homage).\r\n", "\r\n", "\t-f\tMinimum overlap required as a fraction of A.\r\n", "\t\t- Default is 1E-9 (i.e., 1bp).\r\n", "\t\t- FLOAT (e.g. 0.50)\r\n", "\r\n", "\t-r\tRequire that the fraction overlap be reciprocal for A and B.\r\n", "\t\t- In other words, if -f is 0.90 and -r is used, this requires\r\n", "\t\t that B overlap 90% of A and A _also_ overlaps 90% of B.\r\n", "\r\n", "\t-s\tRequire same strandedness. That is, only report hits in B\r\n", "\t\tthat overlap A on the _same_ strand.\r\n", "\t\t- By default, overlaps are reported without respect to strand.\r\n", "\r\n", "\t-S\tRequire different strandedness. That is, only report hits in B\r\n", "\t\tthat overlap A on the _opposite_ strand.\r\n", "\t\t- By default, overlaps are reported without respect to strand.\r\n", "\r\n", "\t-split\tTreat \"split\" BAM or BED12 entries as distinct BED intervals.\r\n", "\r\n", "\t-sorted\tUse the \"chromsweep\" algorithm for sorted (-k1,1 -k2,2n) input\r", "\r\n", "\r\n", "\t-header\tPrint the header from the A file prior to results.\r\n", "\r\n", "Notes: \r\n", "\t(1) When a BAM file is used for the A file, the alignment is retained if overlaps exist,\r\n", "\tand exlcuded if an overlap cannot be found. If multiple overlaps exist, they are not\r\n", "\treported, as we are only testing for one or more overlaps.\r\n", "\r\n" ] } ], "source": [ "!{bedtoolsDirectory}intersectBed -h" ] }, { "cell_type": "code", "execution_count": 41, "metadata": { "collapsed": false }, "outputs": [], "source": [ "!{bedtoolsDirectory}intersectBed \\\n", "-u \\\n", "-a {mcCGMotifs} \\\n", "-b {mcGenes} \\\n", "> Mcap-CGMotif-Gene-Overlaps.txt" ] }, { "cell_type": "code", "execution_count": 42, "metadata": { "collapsed": false }, "outputs": [], "source": [ "!{bedtoolsDirectory}intersectBed \\\n", "-u \\\n", "-a {mcCGMotifs} \\\n", "-b {mcCDS} \\\n", "> Mcap-CGMotif-CDS-Overlaps.txt" ] }, { "cell_type": "code", "execution_count": 43, "metadata": { "collapsed": false }, "outputs": [], "source": [ "!{bedtoolsDirectory}intersectBed \\\n", "-u \\\n", "-a {mcCGMotifs} \\\n", "-b {mcIntron} \\\n", "> Mcap-CGMotif-Intron-Overlaps.txt" ] }, { "cell_type": "code", "execution_count": 44, "metadata": { "collapsed": false }, "outputs": [], "source": [ "!{bedtoolsDirectory}intersectBed \\\n", "-u \\\n", "-a {mcCGMotifs} \\\n", "-b {mcFlanks} \\\n", "> Mcap-CGMotif-Flanks-Overlaps.txt" ] }, { "cell_type": "code", "execution_count": 45, "metadata": { "collapsed": false }, "outputs": [], "source": [ "!{bedtoolsDirectory}intersectBed \\\n", "-u \\\n", "-a {mcCGMotifs} \\\n", "-b {mcUpstream} \\\n", "> Mcap-CGMotif-Flanks-Upstream-Overlaps.txt" ] }, { "cell_type": "code", "execution_count": 46, "metadata": { "collapsed": false }, "outputs": [], "source": [ "!{bedtoolsDirectory}intersectBed \\\n", "-u \\\n", "-a {mcCGMotifs} \\\n", "-b {mcDownstream} \\\n", "> Mcap-CGMotif-Flanks-Downstream-Overlaps.txt" ] }, { "cell_type": "code", "execution_count": 47, "metadata": { "collapsed": false, "scrolled": true }, "outputs": [], "source": [ "!{bedtoolsDirectory}intersectBed \\\n", "-u \\\n", "-a {mcCGMotifs} \\\n", "-b {mcIntergenic} \\\n", "> Mcap-CGMotif-Intergenic-Overlaps.txt" ] }, { "cell_type": "code", "execution_count": 48, "metadata": { "collapsed": false }, "outputs": [], "source": [ "!wc -l *CGMotif* > Mcap-CGMotif-Overlaps-counts.txt" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "### 2. Download coverage files" ] }, { "cell_type": "code", "execution_count": 33, "metadata": { "collapsed": false, "scrolled": true }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "--2020-07-09 09:45:58-- https://gannet.fish.washington.edu/seashell/bu-mox/scrubbed/031520-TG-bs/Mcap_tg/dedup/\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", "HTTP request sent, awaiting response... 200 OK\n", "Length: unspecified [text/html]\n", "Saving to: ‘gannet.fish.washington.edu/seashell/bu-mox/scrubbed/031520-TG-bs/Mcap_tg/dedup/index.html.tmp’\n", "\n", "gannet.fish.washing [ <=> ] 42.27K --.-KB/s in 0.001s \n", "\n", "2020-07-09 09:45:59 (32.5 MB/s) - ‘gannet.fish.washington.edu/seashell/bu-mox/scrubbed/031520-TG-bs/Mcap_tg/dedup/index.html.tmp’ saved [43285]\n", "\n", "Loading robots.txt; please ignore errors.\n", "--2020-07-09 09:45:59-- 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", "2020-07-09 09:45:59 ERROR 404: Not Found.\n", "\n", "Removing gannet.fish.washington.edu/seashell/bu-mox/scrubbed/031520-TG-bs/Mcap_tg/dedup/index.html.tmp since it should be rejected.\n", "\n", "--2020-07-09 09:45:59-- https://gannet.fish.washington.edu/seashell/bu-mox/scrubbed/031520-TG-bs/Mcap_tg/dedup/?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: ‘gannet.fish.washington.edu/seashell/bu-mox/scrubbed/031520-TG-bs/Mcap_tg/dedup/index.html?C=N;O=D.tmp’\n", "\n", "gannet.fish.washing [ <=> ] 42.27K --.-KB/s in 0.001s \n", "\n", "2020-07-09 09:46:00 (27.7 MB/s) - ‘gannet.fish.washington.edu/seashell/bu-mox/scrubbed/031520-TG-bs/Mcap_tg/dedup/index.html?C=N;O=D.tmp’ saved [43285]\n", "\n", "Removing gannet.fish.washington.edu/seashell/bu-mox/scrubbed/031520-TG-bs/Mcap_tg/dedup/index.html?C=N;O=D.tmp since it should be rejected.\n", "\n", "--2020-07-09 09:46:00-- https://gannet.fish.washington.edu/seashell/bu-mox/scrubbed/031520-TG-bs/Mcap_tg/dedup/?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: ‘gannet.fish.washington.edu/seashell/bu-mox/scrubbed/031520-TG-bs/Mcap_tg/dedup/index.html?C=M;O=A.tmp’\n", "\n", "gannet.fish.washing [ <=> ] 42.27K --.-KB/s in 0.002s \n", "\n", "2020-07-09 09:46:01 (27.0 MB/s) - ‘gannet.fish.washington.edu/seashell/bu-mox/scrubbed/031520-TG-bs/Mcap_tg/dedup/index.html?C=M;O=A.tmp’ saved [43285]\n", "\n", "Removing gannet.fish.washington.edu/seashell/bu-mox/scrubbed/031520-TG-bs/Mcap_tg/dedup/index.html?C=M;O=A.tmp since it should be rejected.\n", "\n", "--2020-07-09 09:46:01-- https://gannet.fish.washington.edu/seashell/bu-mox/scrubbed/031520-TG-bs/Mcap_tg/dedup/?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: ‘gannet.fish.washington.edu/seashell/bu-mox/scrubbed/031520-TG-bs/Mcap_tg/dedup/index.html?C=S;O=A.tmp’\n", "\n", "gannet.fish.washing [ <=> ] 42.27K --.-KB/s in 0.001s \n", "\n", "2020-07-09 09:46:02 (28.4 MB/s) - ‘gannet.fish.washington.edu/seashell/bu-mox/scrubbed/031520-TG-bs/Mcap_tg/dedup/index.html?C=S;O=A.tmp’ saved [43285]\n", "\n", "Removing gannet.fish.washington.edu/seashell/bu-mox/scrubbed/031520-TG-bs/Mcap_tg/dedup/index.html?C=S;O=A.tmp since it should be rejected.\n", "\n", "--2020-07-09 09:46:02-- https://gannet.fish.washington.edu/seashell/bu-mox/scrubbed/031520-TG-bs/Mcap_tg/dedup/?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: ‘gannet.fish.washington.edu/seashell/bu-mox/scrubbed/031520-TG-bs/Mcap_tg/dedup/index.html?C=D;O=A.tmp’\n", "\n", "gannet.fish.washing [ <=> ] 42.27K --.-KB/s in 0.002s \n", "\n", "2020-07-09 09:46:03 (26.3 MB/s) - ‘gannet.fish.washington.edu/seashell/bu-mox/scrubbed/031520-TG-bs/Mcap_tg/dedup/index.html?C=D;O=A.tmp’ saved [43285]\n", "\n", "Removing gannet.fish.washington.edu/seashell/bu-mox/scrubbed/031520-TG-bs/Mcap_tg/dedup/index.html?C=D;O=A.tmp since it should be rejected.\n", "\n", "--2020-07-09 09:46:03-- https://gannet.fish.washington.edu/seashell/bu-mox/scrubbed/031520-TG-bs/Mcap_tg/dedup/Meth10_R1_001_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: 123101388 (117M)\n", "Saving to: ‘gannet.fish.washington.edu/seashell/bu-mox/scrubbed/031520-TG-bs/Mcap_tg/dedup/Meth10_R1_001_val_1_bismark_bt2_pe._5x.bedgraph’\n", "\n", "gannet.fish.washing 100%[===================>] 117.40M 79.2MB/s in 1.5s \n", "\n", "2020-07-09 09:46:05 (79.2 MB/s) - ‘gannet.fish.washington.edu/seashell/bu-mox/scrubbed/031520-TG-bs/Mcap_tg/dedup/Meth10_R1_001_val_1_bismark_bt2_pe._5x.bedgraph’ saved [123101388/123101388]\n", "\n", "--2020-07-09 09:46:05-- https://gannet.fish.washington.edu/seashell/bu-mox/scrubbed/031520-TG-bs/Mcap_tg/dedup/Meth11_R1_001_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: 125607408 (120M)\n", "Saving to: ‘gannet.fish.washington.edu/seashell/bu-mox/scrubbed/031520-TG-bs/Mcap_tg/dedup/Meth11_R1_001_val_1_bismark_bt2_pe._5x.bedgraph’\n", "\n", "gannet.fish.washing 100%[===================>] 119.79M 78.6MB/s in 1.5s \n", "\n", "2020-07-09 09:46:06 (78.6 MB/s) - ‘gannet.fish.washington.edu/seashell/bu-mox/scrubbed/031520-TG-bs/Mcap_tg/dedup/Meth11_R1_001_val_1_bismark_bt2_pe._5x.bedgraph’ saved [125607408/125607408]\n", "\n", "--2020-07-09 09:46:06-- https://gannet.fish.washington.edu/seashell/bu-mox/scrubbed/031520-TG-bs/Mcap_tg/dedup/Meth12_R1_001_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: 236954482 (226M)\n", "Saving to: ‘gannet.fish.washington.edu/seashell/bu-mox/scrubbed/031520-TG-bs/Mcap_tg/dedup/Meth12_R1_001_val_1_bismark_bt2_pe._5x.bedgraph’\n", "\n", "gannet.fish.washing 100%[===================>] 225.98M 70.9MB/s in 3.2s \n", "\n", "2020-07-09 09:46:10 (70.9 MB/s) - ‘gannet.fish.washington.edu/seashell/bu-mox/scrubbed/031520-TG-bs/Mcap_tg/dedup/Meth12_R1_001_val_1_bismark_bt2_pe._5x.bedgraph’ saved [236954482/236954482]\n", "\n", "--2020-07-09 09:46:10-- https://gannet.fish.washington.edu/seashell/bu-mox/scrubbed/031520-TG-bs/Mcap_tg/dedup/Meth16_R1_001_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: 15778525 (15M)\n", "Saving to: ‘gannet.fish.washington.edu/seashell/bu-mox/scrubbed/031520-TG-bs/Mcap_tg/dedup/Meth16_R1_001_val_1_bismark_bt2_pe._5x.bedgraph’\n", "\n", "gannet.fish.washing 100%[===================>] 15.05M --.-KB/s in 0.1s \n", "\n", "2020-07-09 09:46:10 (102 MB/s) - ‘gannet.fish.washington.edu/seashell/bu-mox/scrubbed/031520-TG-bs/Mcap_tg/dedup/Meth16_R1_001_val_1_bismark_bt2_pe._5x.bedgraph’ saved [15778525/15778525]\n", "\n", "--2020-07-09 09:46:10-- https://gannet.fish.washington.edu/seashell/bu-mox/scrubbed/031520-TG-bs/Mcap_tg/dedup/Meth17_R1_001_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: 6552639 (6.2M)\n", "Saving to: ‘gannet.fish.washington.edu/seashell/bu-mox/scrubbed/031520-TG-bs/Mcap_tg/dedup/Meth17_R1_001_val_1_bismark_bt2_pe._5x.bedgraph’\n", "\n", "gannet.fish.washing 100%[===================>] 6.25M --.-KB/s in 0.08s \n", "\n", "2020-07-09 09:46:10 (82.2 MB/s) - ‘gannet.fish.washington.edu/seashell/bu-mox/scrubbed/031520-TG-bs/Mcap_tg/dedup/Meth17_R1_001_val_1_bismark_bt2_pe._5x.bedgraph’ saved [6552639/6552639]\n", "\n", "--2020-07-09 09:46:10-- https://gannet.fish.washington.edu/seashell/bu-mox/scrubbed/031520-TG-bs/Mcap_tg/dedup/Meth18_R1_001_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: 4146851 (4.0M)\n", "Saving to: ‘gannet.fish.washington.edu/seashell/bu-mox/scrubbed/031520-TG-bs/Mcap_tg/dedup/Meth18_R1_001_val_1_bismark_bt2_pe._5x.bedgraph’\n", "\n", "gannet.fish.washing 100%[===================>] 3.95M --.-KB/s in 0.04s \n", "\n", "2020-07-09 09:46:10 (91.8 MB/s) - ‘gannet.fish.washington.edu/seashell/bu-mox/scrubbed/031520-TG-bs/Mcap_tg/dedup/Meth18_R1_001_val_1_bismark_bt2_pe._5x.bedgraph’ saved [4146851/4146851]\n", "\n", "FINISHED --2020-07-09 09:46:10--\n", "Total wall clock time: 12s\n", "Downloaded: 11 files, 489M in 6.5s (75.5 MB/s)\n" ] } ], "source": [ "#Download Mcap WGBS and MBD-BS 5x sample bedgraphs\n", "!wget -r -l1 --no-parent -A \"*5x.bedgraph\" https://gannet.fish.washington.edu/seashell/bu-mox/scrubbed/031520-TG-bs/Mcap_tg/dedup/" ] }, { "cell_type": "code", "execution_count": 34, "metadata": { "collapsed": true }, "outputs": [], "source": [ "#Move samples from directory structure on gannet to cd\n", "!mv gannet.fish.washington.edu/seashell/bu-mox/scrubbed/031520-TG-bs/Mcap_tg/dedup/* ." ] }, { "cell_type": "code", "execution_count": 35, "metadata": { "collapsed": true }, "outputs": [], "source": [ "#Remove empty directory\n", "!rm -r gannet.fish.washington.edu/" ] }, { "cell_type": "code", "execution_count": 36, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "Meth10_R1_001_val_1_bismark_bt2_pe._5x.bedgraph\r\n", "Meth11_R1_001_val_1_bismark_bt2_pe._5x.bedgraph\r\n", "Meth12_R1_001_val_1_bismark_bt2_pe._5x.bedgraph\r\n", "Meth16_R1_001_val_1_bismark_bt2_pe._5x.bedgraph\r\n", "Meth17_R1_001_val_1_bismark_bt2_pe._5x.bedgraph\r\n", "Meth18_R1_001_val_1_bismark_bt2_pe._5x.bedgraph\r\n" ] } ], "source": [ "#Check downloaded files\n", "!ls *bedgraph" ] }, { "cell_type": "code", "execution_count": 37, "metadata": { "collapsed": false, "scrolled": true }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "--2020-07-09 09:46:11-- https://gannet.fish.washington.edu/seashell/bu-mox/scrubbed/031520-TG-bs/Mcap_tg/nodedup/\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", "HTTP request sent, awaiting response... 200 OK\n", "Length: unspecified [text/html]\n", "Saving to: ‘gannet.fish.washington.edu/seashell/bu-mox/scrubbed/031520-TG-bs/Mcap_tg/nodedup/index.html.tmp’\n", "\n", "gannet.fish.washing [ <=> ] 19.31K --.-KB/s in 0.001s \n", "\n", "2020-07-09 09:46:11 (32.8 MB/s) - ‘gannet.fish.washington.edu/seashell/bu-mox/scrubbed/031520-TG-bs/Mcap_tg/nodedup/index.html.tmp’ saved [19778]\n", "\n", "Loading robots.txt; please ignore errors.\n", "--2020-07-09 09:46:11-- 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", "2020-07-09 09:46:11 ERROR 404: Not Found.\n", "\n", "Removing gannet.fish.washington.edu/seashell/bu-mox/scrubbed/031520-TG-bs/Mcap_tg/nodedup/index.html.tmp since it should be rejected.\n", "\n", "--2020-07-09 09:46:11-- https://gannet.fish.washington.edu/seashell/bu-mox/scrubbed/031520-TG-bs/Mcap_tg/nodedup/?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: ‘gannet.fish.washington.edu/seashell/bu-mox/scrubbed/031520-TG-bs/Mcap_tg/nodedup/index.html?C=N;O=D.tmp’\n", "\n", "gannet.fish.washing [ <=> ] 19.31K --.-KB/s in 0s \n", "\n", "2020-07-09 09:46:12 (48.7 MB/s) - ‘gannet.fish.washington.edu/seashell/bu-mox/scrubbed/031520-TG-bs/Mcap_tg/nodedup/index.html?C=N;O=D.tmp’ saved [19778]\n", "\n", "Removing gannet.fish.washington.edu/seashell/bu-mox/scrubbed/031520-TG-bs/Mcap_tg/nodedup/index.html?C=N;O=D.tmp since it should be rejected.\n", "\n", "--2020-07-09 09:46:12-- https://gannet.fish.washington.edu/seashell/bu-mox/scrubbed/031520-TG-bs/Mcap_tg/nodedup/?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: ‘gannet.fish.washington.edu/seashell/bu-mox/scrubbed/031520-TG-bs/Mcap_tg/nodedup/index.html?C=M;O=A.tmp’\n", "\n", "gannet.fish.washing [ <=> ] 19.31K --.-KB/s in 0s \n", "\n", "2020-07-09 09:46:12 (50.3 MB/s) - ‘gannet.fish.washington.edu/seashell/bu-mox/scrubbed/031520-TG-bs/Mcap_tg/nodedup/index.html?C=M;O=A.tmp’ saved [19778]\n", "\n", "Removing gannet.fish.washington.edu/seashell/bu-mox/scrubbed/031520-TG-bs/Mcap_tg/nodedup/index.html?C=M;O=A.tmp since it should be rejected.\n", "\n", "--2020-07-09 09:46:12-- https://gannet.fish.washington.edu/seashell/bu-mox/scrubbed/031520-TG-bs/Mcap_tg/nodedup/?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: ‘gannet.fish.washington.edu/seashell/bu-mox/scrubbed/031520-TG-bs/Mcap_tg/nodedup/index.html?C=S;O=A.tmp’\n", "\n", "gannet.fish.washing [ <=> ] 19.31K --.-KB/s in 0.001s \n", "\n", "2020-07-09 09:46:12 (25.9 MB/s) - ‘gannet.fish.washington.edu/seashell/bu-mox/scrubbed/031520-TG-bs/Mcap_tg/nodedup/index.html?C=S;O=A.tmp’ saved [19778]\n", "\n", "Removing gannet.fish.washington.edu/seashell/bu-mox/scrubbed/031520-TG-bs/Mcap_tg/nodedup/index.html?C=S;O=A.tmp since it should be rejected.\n", "\n", "--2020-07-09 09:46:12-- https://gannet.fish.washington.edu/seashell/bu-mox/scrubbed/031520-TG-bs/Mcap_tg/nodedup/?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: ‘gannet.fish.washington.edu/seashell/bu-mox/scrubbed/031520-TG-bs/Mcap_tg/nodedup/index.html?C=D;O=A.tmp’\n", "\n", "gannet.fish.washing [ <=> ] 19.31K --.-KB/s in 0.001s \n", "\n", "2020-07-09 09:46:13 (28.6 MB/s) - ‘gannet.fish.washington.edu/seashell/bu-mox/scrubbed/031520-TG-bs/Mcap_tg/nodedup/index.html?C=D;O=A.tmp’ saved [19778]\n", "\n", "Removing gannet.fish.washington.edu/seashell/bu-mox/scrubbed/031520-TG-bs/Mcap_tg/nodedup/index.html?C=D;O=A.tmp since it should be rejected.\n", "\n", "--2020-07-09 09:46:13-- https://gannet.fish.washington.edu/seashell/bu-mox/scrubbed/031520-TG-bs/Mcap_tg/nodedup/Meth13_R1_001_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: 84952729 (81M)\n", "Saving to: ‘gannet.fish.washington.edu/seashell/bu-mox/scrubbed/031520-TG-bs/Mcap_tg/nodedup/Meth13_R1_001_val_1_bismark_bt2_pe._5x.bedgraph’\n", "\n", "gannet.fish.washing 100%[===================>] 81.02M 103MB/s in 0.8s \n", "\n", "2020-07-09 09:46:14 (103 MB/s) - ‘gannet.fish.washington.edu/seashell/bu-mox/scrubbed/031520-TG-bs/Mcap_tg/nodedup/Meth13_R1_001_val_1_bismark_bt2_pe._5x.bedgraph’ saved [84952729/84952729]\n", "\n", "--2020-07-09 09:46:14-- https://gannet.fish.washington.edu/seashell/bu-mox/scrubbed/031520-TG-bs/Mcap_tg/nodedup/Meth14_R1_001_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: 70900427 (68M)\n", "Saving to: ‘gannet.fish.washington.edu/seashell/bu-mox/scrubbed/031520-TG-bs/Mcap_tg/nodedup/Meth14_R1_001_val_1_bismark_bt2_pe._5x.bedgraph’\n", "\n", "gannet.fish.washing 100%[===================>] 67.62M 85.3MB/s in 0.8s \n", "\n", "2020-07-09 09:46:15 (85.3 MB/s) - ‘gannet.fish.washington.edu/seashell/bu-mox/scrubbed/031520-TG-bs/Mcap_tg/nodedup/Meth14_R1_001_val_1_bismark_bt2_pe._5x.bedgraph’ saved [70900427/70900427]\n", "\n", "--2020-07-09 09:46:15-- https://gannet.fish.washington.edu/seashell/bu-mox/scrubbed/031520-TG-bs/Mcap_tg/nodedup/Meth15_R1_001_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: 85048595 (81M)\n", "Saving to: ‘gannet.fish.washington.edu/seashell/bu-mox/scrubbed/031520-TG-bs/Mcap_tg/nodedup/Meth15_R1_001_val_1_bismark_bt2_pe._5x.bedgraph’\n", "\n", "gannet.fish.washing 100%[===================>] 81.11M 104MB/s in 0.8s \n", "\n", "2020-07-09 09:46:15 (104 MB/s) - ‘gannet.fish.washington.edu/seashell/bu-mox/scrubbed/031520-TG-bs/Mcap_tg/nodedup/Meth15_R1_001_val_1_bismark_bt2_pe._5x.bedgraph’ saved [85048595/85048595]\n", "\n", "FINISHED --2020-07-09 09:46:15--\n", "Total wall clock time: 4.6s\n", "Downloaded: 8 files, 230M in 2.4s (97.3 MB/s)\n" ] } ], "source": [ "#Download Mcap RRBS 5x sample bedgraphs\n", "!wget -r -l1 --no-parent -A \"*5x.bedgraph\" https://gannet.fish.washington.edu/seashell/bu-mox/scrubbed/031520-TG-bs/Mcap_tg/nodedup/" ] }, { "cell_type": "code", "execution_count": 38, "metadata": { "collapsed": true }, "outputs": [], "source": [ "#Move samples from directory structure on gannet to cd\n", "!mv gannet.fish.washington.edu/seashell/bu-mox/scrubbed/031520-TG-bs/Mcap_tg/nodedup/* ." ] }, { "cell_type": "code", "execution_count": 39, "metadata": { "collapsed": true }, "outputs": [], "source": [ "#Remove empty directory\n", "!rm -r gannet.fish.washington.edu/" ] }, { "cell_type": "code", "execution_count": 40, "metadata": { "collapsed": false, "scrolled": true }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "Meth10_R1_001_val_1_bismark_bt2_pe._5x.bedgraph\r\n", "Meth11_R1_001_val_1_bismark_bt2_pe._5x.bedgraph\r\n", "Meth12_R1_001_val_1_bismark_bt2_pe._5x.bedgraph\r\n", "Meth13_R1_001_val_1_bismark_bt2_pe._5x.bedgraph\r\n", "Meth14_R1_001_val_1_bismark_bt2_pe._5x.bedgraph\r\n", "Meth15_R1_001_val_1_bismark_bt2_pe._5x.bedgraph\r\n", "Meth16_R1_001_val_1_bismark_bt2_pe._5x.bedgraph\r\n", "Meth17_R1_001_val_1_bismark_bt2_pe._5x.bedgraph\r\n", "Meth18_R1_001_val_1_bismark_bt2_pe._5x.bedgraph\r\n" ] } ], "source": [ "!find *bedgraph" ] }, { "cell_type": "code", "execution_count": 41, "metadata": { "collapsed": false, "scrolled": true }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "Meth16_R1_001_val_1_bismark_bt2_pe._5x.bedgraph: OK\n", "Meth12_R1_001_val_1_bismark_bt2_pe._5x.bedgraph: OK\n", "Meth17_R1_001_val_1_bismark_bt2_pe._5x.bedgraph: OK\n", "Meth10_R1_001_val_1_bismark_bt2_pe._5x.bedgraph: OK\n", "Meth18_R1_001_val_1_bismark_bt2_pe._5x.bedgraph: OK\n", "Meth11_R1_001_val_1_bismark_bt2_pe._5x.bedgraph: OK\n", "Meth14_R1_001_val_1_bismark_bt2_pe._5x.bedgraph: OK\n", "Meth15_R1_001_val_1_bismark_bt2_pe._5x.bedgraph: OK\n", "Meth13_R1_001_val_1_bismark_bt2_pe._5x.bedgraph: OK\n" ] } ], "source": [ "#Verify checksums from gannet\n", "!md5sum -c ../Mcap-5xbedgraph-GANNET-md5sum.txt" ] }, { "cell_type": "code", "execution_count": 42, "metadata": { "collapsed": false, "scrolled": true }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ " 4571288 Meth10_R1_001_val_1_bismark_bt2_pe._5x.bedgraph\n", " 4661716 Meth11_R1_001_val_1_bismark_bt2_pe._5x.bedgraph\n", " 8791700 Meth12_R1_001_val_1_bismark_bt2_pe._5x.bedgraph\n", " 3173254 Meth13_R1_001_val_1_bismark_bt2_pe._5x.bedgraph\n", " 2648697 Meth14_R1_001_val_1_bismark_bt2_pe._5x.bedgraph\n", " 3176517 Meth15_R1_001_val_1_bismark_bt2_pe._5x.bedgraph\n", " 583599 Meth16_R1_001_val_1_bismark_bt2_pe._5x.bedgraph\n", " 242390 Meth17_R1_001_val_1_bismark_bt2_pe._5x.bedgraph\n", " 153392 Meth18_R1_001_val_1_bismark_bt2_pe._5x.bedgraph\n", " 28002553 total\n" ] } ], "source": [ "!wc -l *bedgraph" ] }, { "cell_type": "code", "execution_count": 43, "metadata": { "collapsed": true }, "outputs": [], "source": [ "!wc -l *bedgraph > Mcap-5x-bedgraph-counts.txt" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "### 3. Characterize methylation for each CpG dinucleotide\n", "\n", "- Methylated: > 50% methylation\n", "- Sparsely methylated: 10-50% methylation\n", "- Unmethylated: < 10% methylation" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "##### Methylated loci" ] }, { "cell_type": "code", "execution_count": 44, "metadata": { "collapsed": true }, "outputs": [], "source": [ "%%bash\n", "for f in *bedgraph\n", "do\n", " awk '{if ($4 >= 50) { print $1, $2, $3, $4 }}' ${f} \\\n", " > ${f}-Meth\n", "done" ] }, { "cell_type": "code", "execution_count": 45, "metadata": { "collapsed": false, "scrolled": true }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "==> Meth10_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth <==\r\n", "1 58745 58747 100.000000\r\n", "1 103334 103336 100.000000\r\n", "1 103347 103349 100.000000\r\n", "1 103356 103358 100.000000\r\n", "1 103360 103362 100.000000\r\n", "1 103398 103400 100.000000\r\n", "1 105953 105955 80.000000\r\n", "1 106012 106014 50.000000\r\n", "1 106155 106157 60.000000\r\n", "1 106173 106175 66.666667\r\n", "\r\n", "==> Meth11_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth <==\r\n", "1 6905 6907 60.000000\r\n", "1 7273 7275 80.000000\r\n", "1 58745 58747 100.000000\r\n", "1 59207 59209 100.000000\r\n", "1 69235 69237 100.000000\r\n", "1 69271 69273 80.000000\r\n", "1 69275 69277 100.000000\r\n", "1 69451 69453 100.000000\r\n", "1 69580 69582 100.000000\r\n", "1 69584 69586 100.000000\r\n", "\r\n", "==> Meth12_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth <==\r\n", "1 4948 4950 50.000000\r\n", "1 4967 4969 50.000000\r\n", "1 4986 4988 50.000000\r\n", "1 57065 57067 80.000000\r\n", "1 58609 58611 100.000000\r\n", "1 58618 58620 100.000000\r\n", "1 59207 59209 100.000000\r\n", "1 59277 59279 100.000000\r\n", "1 59393 59395 100.000000\r\n", "1 59438 59440 100.000000\r\n", "\r\n", "==> Meth13_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth <==\r\n", "1 58618 58620 100.000000\r\n", "1 58745 58747 97.959184\r\n", "1 58764 58766 100.000000\r\n", "1 58792 58794 92.592593\r\n", "1 66041 66043 100.000000\r\n", "1 66050 66052 100.000000\r\n", "1 66339 66341 88.888889\r\n", "1 66345 66347 77.777778\r\n", "1 66354 66356 77.777778\r\n", "1 66400 66402 100.000000\r\n", "\r\n", "==> Meth14_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth <==\r\n", "1 32228 32230 100.000000\r\n", "1 58618 58620 94.117647\r\n", "1 58745 58747 100.000000\r\n", "1 58764 58766 100.000000\r\n", "1 58792 58794 100.000000\r\n", "1 105822 105824 100.000000\r\n", "1 105825 105827 100.000000\r\n", "1 105836 105838 100.000000\r\n", "1 105874 105876 100.000000\r\n", "1 105883 105885 87.500000\r\n", "\r\n", "==> Meth15_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth <==\r\n", "1 58618 58620 92.857143\r\n", "1 58745 58747 92.500000\r\n", "1 58764 58766 97.500000\r\n", "1 58792 58794 57.692308\r\n", "1 101462 101464 90.476190\r\n", "1 101535 101537 100.000000\r\n", "1 108751 108753 100.000000\r\n", "1 108778 108780 100.000000\r\n", "1 108787 108789 82.758621\r\n", "1 108803 108805 100.000000\r\n", "\r\n", "==> Meth16_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth <==\r\n", "1 344031 344033 50.000000\r\n", "1 344044 344046 60.000000\r\n", "1 446326 446328 80.000000\r\n", "1 446344 446346 100.000000\r\n", "1 446367 446369 100.000000\r\n", "1 446376 446378 100.000000\r\n", "1 786125 786127 60.000000\r\n", "1 786144 786146 100.000000\r\n", "1 786151 786153 100.000000\r\n", "1 789213 789215 60.000000\r\n", "\r\n", "==> Meth17_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth <==\r\n", "1 59438 59440 100.000000\r\n", "1 106173 106175 100.000000\r\n", "1 106202 106204 100.000000\r\n", "1 1243019 1243021 60.000000\r\n", "1 1409734 1409736 100.000000\r\n", "1 1419093 1419095 87.500000\r\n", "1 1457412 1457414 100.000000\r\n", "1 1457444 1457446 80.000000\r\n", "1 1457447 1457449 100.000000\r\n", "1 1457450 1457452 100.000000\r\n", "\r\n", "==> Meth18_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth <==\r\n", "1 1002973 1002975 50.000000\r\n", "1 1343240 1343242 100.000000\r\n", "1 1343249 1343251 100.000000\r\n", "1 1343263 1343265 83.333333\r\n", "1 1343265 1343267 100.000000\r\n", "1 1343295 1343297 100.000000\r\n", "1 1343304 1343306 100.000000\r\n", "1 1343320 1343322 100.000000\r\n", "1 1451821 1451823 60.000000\r\n", "1 1468323 1468325 100.000000\r\n" ] } ], "source": [ "!head *Meth" ] }, { "cell_type": "code", "execution_count": 46, "metadata": { "collapsed": false, "scrolled": true }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ " 450582 Meth10_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth\n", " 528902 Meth11_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth\n", " 1059904 Meth12_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth\n", " 257741 Meth13_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth\n", " 184742 Meth14_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth\n", " 231347 Meth15_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth\n", " 106695 Meth16_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth\n", " 45506 Meth17_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth\n", " 29468 Meth18_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth\n", " 2894887 total\n" ] } ], "source": [ "!wc -l *-Meth" ] }, { "cell_type": "code", "execution_count": 47, "metadata": { "collapsed": true }, "outputs": [], "source": [ "!wc -l *-Meth > Mcap-5x-Meth-counts.txt" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "##### Sparsely methylated loci" ] }, { "cell_type": "code", "execution_count": 48, "metadata": { "collapsed": true }, "outputs": [], "source": [ "%%bash\n", "for f in *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": 49, "metadata": { "collapsed": false, "scrolled": true }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "==> Meth10_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth <==\r\n", "1 27782 27784 20.000000\r\n", "1 80133 80135 20.000000\r\n", "1 106202 106204 40.000000\r\n", "1 140551 140553 33.333333\r\n", "1 148080 148082 16.666667\r\n", "1 150099 150101 40.000000\r\n", "1 169735 169737 12.500000\r\n", "1 169771 169773 42.857143\r\n", "1 169796 169798 14.285714\r\n", "1 169800 169802 16.666667\r\n", "\r\n", "==> Meth11_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth <==\r\n", "1 6550 6552 12.500000\r\n", "1 6671 6673 20.000000\r\n", "1 6996 6998 20.000000\r\n", "1 7016 7018 40.000000\r\n", "1 7019 7021 40.000000\r\n", "1 7293 7295 16.666667\r\n", "1 7427 7429 16.666667\r\n", "1 74928 74930 14.285714\r\n", "1 153767 153769 20.000000\r\n", "1 193930 193932 20.000000\r\n", "\r\n", "==> Meth12_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth <==\r\n", "1 4190 4192 16.666667\r\n", "1 4891 4893 33.333333\r\n", "1 4910 4912 28.571429\r\n", "1 4929 4931 33.333333\r\n", "1 5005 5007 28.571429\r\n", "1 5024 5026 40.000000\r\n", "1 5151 5153 20.000000\r\n", "1 5160 5162 16.666667\r\n", "1 5228 5230 11.111111\r\n", "1 6282 6284 11.111111\r\n", "\r\n", "==> Meth13_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth <==\r\n", "1 15092 15094 30.000000\r\n", "1 21739 21741 13.636364\r\n", "1 34139 34141 11.764706\r\n", "1 45163 45165 10.317460\r\n", "1 48370 48372 14.285714\r\n", "1 87492 87494 33.333333\r\n", "1 89011 89013 14.285714\r\n", "1 169847 169849 12.820513\r\n", "1 198078 198080 30.434783\r\n", "1 203991 203993 12.500000\r\n", "\r\n", "==> Meth14_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth <==\r\n", "1 124833 124835 20.000000\r\n", "1 135853 135855 33.333333\r\n", "1 166013 166015 12.500000\r\n", "1 227400 227402 11.200000\r\n", "1 230854 230856 14.285714\r\n", "1 246955 246957 29.545455\r\n", "1 248898 248900 13.333333\r\n", "1 249322 249324 42.857143\r\n", "1 257203 257205 14.285714\r\n", "1 305489 305491 11.111111\r\n", "\r\n", "==> Meth15_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth <==\r\n", "1 41916 41918 13.043478\r\n", "1 42261 42263 16.666667\r\n", "1 78269 78271 22.222222\r\n", "1 101503 101505 31.428571\r\n", "1 101545 101547 40.000000\r\n", "1 169847 169849 14.285714\r\n", "1 169891 169893 11.428571\r\n", "1 169927 169929 20.000000\r\n", "1 169936 169938 22.857143\r\n", "1 170062 170064 21.052632\r\n", "\r\n", "==> Meth16_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth <==\r\n", "1 211907 211909 40.000000\r\n", "1 217198 217200 14.285714\r\n", "1 234158 234160 14.285714\r\n", "1 234196 234198 12.500000\r\n", "1 244563 244565 20.000000\r\n", "1 269174 269176 16.666667\r\n", "1 269178 269180 16.666667\r\n", "1 269182 269184 16.666667\r\n", "1 284269 284271 16.666667\r\n", "1 323095 323097 16.666667\r\n", "\r\n", "==> Meth17_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth <==\r\n", "1 376177 376179 16.666667\r\n", "1 460920 460922 40.000000\r\n", "1 460947 460949 33.333333\r\n", "1 460953 460955 33.333333\r\n", "1 461051 461053 20.000000\r\n", "1 519486 519488 28.571429\r\n", "1 519505 519507 33.333333\r\n", "1 601511 601513 20.000000\r\n", "1 618190 618192 16.666667\r\n", "1 618205 618207 14.285714\r\n", "\r\n", "==> Meth18_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth <==\r\n", "1 8113 8115 20.000000\r\n", "1 277994 277996 16.666667\r\n", "1 387294 387296 20.000000\r\n", "1 461787 461789 40.000000\r\n", "1 480696 480698 20.000000\r\n", "1 605019 605021 28.571429\r\n", "1 605050 605052 33.333333\r\n", "1 646162 646164 20.000000\r\n", "1 667790 667792 40.000000\r\n", "1 726420 726422 20.000000\r\n" ] } ], "source": [ "!head *sparseMeth" ] }, { "cell_type": "code", "execution_count": 50, "metadata": { "collapsed": false, "scrolled": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ " 547868 Meth10_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth\n", " 517805 Meth11_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth\n", " 1000337 Meth12_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth\n", " 152042 Meth13_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth\n", " 135052 Meth14_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth\n", " 179454 Meth15_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth\n", " 74839 Meth16_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth\n", " 28850 Meth17_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth\n", " 16793 Meth18_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth\n", " 2653040 total\n" ] } ], "source": [ "!wc -l *sparseMeth" ] }, { "cell_type": "code", "execution_count": 51, "metadata": { "collapsed": true }, "outputs": [], "source": [ "!wc -l *-sparseMeth > Mcap-5x-sparseMeth-counts.txt" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "##### Unmethylated loci" ] }, { "cell_type": "code", "execution_count": 52, "metadata": { "collapsed": true }, "outputs": [], "source": [ "%%bash\n", "for f in *bedgraph\n", "do\n", " awk '{if ($4 <= 10) { print $1, $2, $3, $4 }}' ${f} \\\n", " > ${f}-unMeth\n", "done" ] }, { "cell_type": "code", "execution_count": 53, "metadata": { "collapsed": false, "scrolled": true }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "==> Meth10_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth <==\r\n", "1 6570 6572 0.000000\r\n", "1 6713 6715 0.000000\r\n", "1 6780 6782 0.000000\r\n", "1 6813 6815 0.000000\r\n", "1 6818 6820 0.000000\r\n", "1 27606 27608 0.000000\r\n", "1 27613 27615 0.000000\r\n", "1 27641 27643 0.000000\r\n", "1 27643 27645 0.000000\r\n", "1 27674 27676 0.000000\r\n", "\r\n", "==> Meth11_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth <==\r\n", "1 4929 4931 0.000000\r\n", "1 5665 5667 0.000000\r\n", "1 6453 6455 0.000000\r\n", "1 6484 6486 0.000000\r\n", "1 6527 6529 0.000000\r\n", "1 6570 6572 0.000000\r\n", "1 6618 6620 0.000000\r\n", "1 6652 6654 0.000000\r\n", "1 6661 6663 0.000000\r\n", "1 6668 6670 0.000000\r\n", "\r\n", "==> Meth12_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth <==\r\n", "1 4062 4064 0.000000\r\n", "1 4069 4071 0.000000\r\n", "1 4077 4079 0.000000\r\n", "1 4086 4088 0.000000\r\n", "1 4146 4148 0.000000\r\n", "1 4150 4152 0.000000\r\n", "1 4155 4157 0.000000\r\n", "1 4172 4174 0.000000\r\n", "1 4184 4186 0.000000\r\n", "1 5043 5045 0.000000\r\n", "\r\n", "==> Meth13_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth <==\r\n", "1 3493 3495 0.000000\r\n", "1 3518 3520 0.000000\r\n", "1 3727 3729 0.000000\r\n", "1 3752 3754 0.000000\r\n", "1 3757 3759 0.000000\r\n", "1 3770 3772 0.000000\r\n", "1 11979 11981 0.000000\r\n", "1 11985 11987 0.000000\r\n", "1 11994 11996 0.000000\r\n", "1 12043 12045 0.000000\r\n", "\r\n", "==> Meth14_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth <==\r\n", "1 3727 3729 0.000000\r\n", "1 3752 3754 0.000000\r\n", "1 3757 3759 0.000000\r\n", "1 3770 3772 0.000000\r\n", "1 11876 11878 0.000000\r\n", "1 11887 11889 0.000000\r\n", "1 11894 11896 0.000000\r\n", "1 11941 11943 0.000000\r\n", "1 11954 11956 0.000000\r\n", "1 11975 11977 0.000000\r\n", "\r\n", "==> Meth15_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth <==\r\n", "1 3493 3495 0.000000\r\n", "1 3518 3520 0.000000\r\n", "1 3727 3729 8.695652\r\n", "1 3752 3754 0.000000\r\n", "1 3757 3759 0.000000\r\n", "1 3770 3772 0.000000\r\n", "1 29753 29755 3.200000\r\n", "1 29821 29823 7.086614\r\n", "1 32243 32245 1.388889\r\n", "1 32283 32285 0.000000\r\n", "\r\n", "==> Meth16_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth <==\r\n", "1 5228 5230 0.000000\r\n", "1 5243 5245 0.000000\r\n", "1 5247 5249 0.000000\r\n", "1 5296 5298 0.000000\r\n", "1 77096 77098 0.000000\r\n", "1 77145 77147 0.000000\r\n", "1 77151 77153 0.000000\r\n", "1 77179 77181 0.000000\r\n", "1 81812 81814 0.000000\r\n", "1 81817 81819 0.000000\r\n", "\r\n", "==> Meth17_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth <==\r\n", "1 210921 210923 0.000000\r\n", "1 210930 210932 0.000000\r\n", "1 219905 219907 0.000000\r\n", "1 229825 229827 0.000000\r\n", "1 229852 229854 0.000000\r\n", "1 231344 231346 0.000000\r\n", "1 233876 233878 0.000000\r\n", "1 233894 233896 0.000000\r\n", "1 255402 255404 0.000000\r\n", "1 271124 271126 0.000000\r\n", "\r\n", "==> Meth18_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth <==\r\n", "1 224609 224611 0.000000\r\n", "1 264560 264562 0.000000\r\n", "1 264598 264600 0.000000\r\n", "1 271145 271147 0.000000\r\n", "1 278004 278006 0.000000\r\n", "1 278039 278041 0.000000\r\n", "1 278049 278051 0.000000\r\n", "1 278067 278069 0.000000\r\n", "1 280413 280415 0.000000\r\n", "1 280448 280450 0.000000\r\n" ] } ], "source": [ "!head *unMeth" ] }, { "cell_type": "code", "execution_count": 54, "metadata": { "collapsed": false, "scrolled": true }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ " 3572838 Meth10_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth\n", " 3615009 Meth11_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth\n", " 6731459 Meth12_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth\n", " 2763471 Meth13_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth\n", " 2328903 Meth14_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth\n", " 2765716 Meth15_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth\n", " 402065 Meth16_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth\n", " 168034 Meth17_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth\n", " 107131 Meth18_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth\n", " 22454626 total\n" ] } ], "source": [ "!wc -l *unMeth" ] }, { "cell_type": "code", "execution_count": 55, "metadata": { "collapsed": true }, "outputs": [], "source": [ "!wc -l *-unMeth > Mcap-5x-unMeth-counts.txt" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "### 4. Characterize genomic locations of CpGs" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "#### 4a. Create BEDfiles" ] }, { "cell_type": "code", "execution_count": 104, "metadata": { "collapsed": false, "scrolled": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ " 4571288 Meth10_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed\n", " 4661716 Meth11_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed\n", " 8791700 Meth12_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed\n", " 3173254 Meth13_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed\n", " 2648697 Meth14_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed\n", " 3176517 Meth15_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed\n", " 583599 Meth16_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed\n", " 242390 Meth17_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed\n", " 153392 Meth18_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed\n" ] } ], "source": [ "%%bash\n", "\n", "for f in *bedgraph\n", "do\n", " awk '{print $1\"\\t\"$2\"\\t\"$3\"\\t\"$4}' ${f} > ${f}.bed\n", " wc -l ${f}.bed\n", "done" ] }, { "cell_type": "code", "execution_count": 110, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ " 450582 Meth10_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed\n", " 528902 Meth11_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed\n", " 1059904 Meth12_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed\n", " 257741 Meth13_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed\n", " 184742 Meth14_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed\n", " 231347 Meth15_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed\n", " 106695 Meth16_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed\n", " 45506 Meth17_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed\n", " 29468 Meth18_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed\n" ] } ], "source": [ "%%bash\n", "\n", "for f in *bedgraph-Meth\n", "do\n", " awk '{print $1\"\\t\"$2\"\\t\"$3\"\\t\"$4}' ${f} > ${f}.bed\n", " wc -l ${f}.bed\n", "done" ] }, { "cell_type": "code", "execution_count": 111, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ " 547868 Meth10_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed\n", " 517805 Meth11_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed\n", " 1000337 Meth12_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed\n", " 152042 Meth13_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed\n", " 135052 Meth14_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed\n", " 179454 Meth15_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed\n", " 74839 Meth16_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed\n", " 28850 Meth17_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed\n", " 16793 Meth18_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed\n" ] } ], "source": [ "%%bash\n", "\n", "for f in *bedgraph-sparseMeth\n", "do\n", " awk '{print $1\"\\t\"$2\"\\t\"$3\"\\t\"$4}' ${f} > ${f}.bed\n", " wc -l ${f}.bed\n", "done" ] }, { "cell_type": "code", "execution_count": 112, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ " 3572838 Meth10_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed\n", " 3615009 Meth11_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed\n", " 6731459 Meth12_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed\n", " 2763471 Meth13_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed\n", " 2328903 Meth14_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed\n", " 2765716 Meth15_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed\n", " 402065 Meth16_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed\n", " 168034 Meth17_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed\n", " 107131 Meth18_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed\n" ] } ], "source": [ "%%bash\n", "\n", "for f in *bedgraph-unMeth\n", "do\n", " awk '{print $1\"\\t\"$2\"\\t\"$3\"\\t\"$4}' ${f} > ${f}.bed\n", " wc -l ${f}.bed\n", "done" ] }, { "cell_type": "code", "execution_count": 113, "metadata": { "collapsed": false, "scrolled": true }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "Meth10_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed\r\n", "Meth10_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed\r\n", "Meth10_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed\r\n", "Meth10_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed\r\n", "Meth11_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed\r\n", "Meth11_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed\r\n", "Meth11_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed\r\n", "Meth11_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed\r\n", "Meth12_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed\r\n", "Meth12_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed\r\n", "Meth12_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed\r\n", "Meth12_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed\r\n", "Meth13_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed\r\n", "Meth13_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed\r\n", "Meth13_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed\r\n", "Meth13_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed\r\n", "Meth14_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed\r\n", "Meth14_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed\r\n", "Meth14_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed\r\n", "Meth14_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed\r\n", "Meth15_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed\r\n", "Meth15_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed\r\n", "Meth15_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed\r\n", "Meth15_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed\r\n", "Meth16_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed\r\n", "Meth16_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed\r\n", "Meth16_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed\r\n", "Meth16_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed\r\n", "Meth17_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed\r\n", "Meth17_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed\r\n", "Meth17_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed\r\n", "Meth17_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed\r\n", "Meth18_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed\r\n", "Meth18_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed\r\n", "Meth18_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed\r\n", "Meth18_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed\r\n" ] } ], "source": [ "#Confirm BEDfile creation\n", "!find *.bed" ] }, { "cell_type": "code", "execution_count": 114, "metadata": { "collapsed": false, "scrolled": true }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "1\t6570\t6572\t0.000000\r\n", "1\t6713\t6715\t0.000000\r\n", "1\t6780\t6782\t0.000000\r\n", "1\t6813\t6815\t0.000000\r\n", "1\t6818\t6820\t0.000000\r\n", "1\t27606\t27608\t0.000000\r\n", "1\t27613\t27615\t0.000000\r\n", "1\t27641\t27643\t0.000000\r\n", "1\t27643\t27645\t0.000000\r\n", "1\t27674\t27676\t0.000000\r\n" ] } ], "source": [ "#Confirm file creation\n", "!head Meth10_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "#### 4b. Genes" ] }, { "cell_type": "code", "execution_count": 115, "metadata": { "collapsed": true, "scrolled": true }, "outputs": [], "source": [ "%%bash\n", "\n", "for f in *bed\n", "do\n", " /usr/local/bin/intersectBed \\\n", " -u \\\n", " -a ${f} \\\n", " -b ../../../genome-feature-files/Mcap.GFFannotation.gene.gff \\\n", " > ${f}-mcGenes\n", "done" ] }, { "cell_type": "code", "execution_count": 116, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "==> Meth10_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-mcGenes <==\r\n", "1\t58745\t58747\t100.000000\r\n", "1\t103334\t103336\t100.000000\r\n", "1\t103347\t103349\t100.000000\r\n", "1\t103356\t103358\t100.000000\r\n", "1\t103360\t103362\t100.000000\r\n", "1\t103398\t103400\t100.000000\r\n", "1\t105953\t105955\t80.000000\r\n", "1\t106012\t106014\t50.000000\r\n", "1\t106155\t106157\t60.000000\r\n", "1\t106173\t106175\t66.666667\r\n", "\r\n", "==> Meth10_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-mcGenes <==\r\n", "1\t80133\t80135\t20.000000\r\n", "1\t106202\t106204\t40.000000\r\n", "1\t184227\t184229\t16.666667\r\n", "1\t184266\t184268\t16.666667\r\n", "1\t184271\t184273\t16.666667\r\n", "1\t238091\t238093\t12.500000\r\n", "1\t307885\t307887\t20.000000\r\n", "1\t323373\t323375\t14.285714\r\n", "1\t324004\t324006\t12.500000\r\n", "1\t324495\t324497\t16.666667\r\n", "\r\n", "==> Meth10_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-mcGenes <==\r\n", "1\t42893\t42895\t0.000000\r\n", "1\t42959\t42961\t0.000000\r\n", "1\t42970\t42972\t0.000000\r\n", "1\t42977\t42979\t0.000000\r\n", "1\t43005\t43007\t0.000000\r\n", "1\t75959\t75961\t0.000000\r\n", "1\t75962\t75964\t0.000000\r\n", "1\t75993\t75995\t0.000000\r\n", "1\t75996\t75998\t0.000000\r\n", "1\t80015\t80017\t0.000000\r\n", "\r\n", "==> Meth10_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-mcGenes <==\r\n", "1\t42893\t42895\t0.000000\r\n", "1\t42959\t42961\t0.000000\r\n", "1\t42970\t42972\t0.000000\r\n", "1\t42977\t42979\t0.000000\r\n", "1\t43005\t43007\t0.000000\r\n", "1\t58745\t58747\t100.000000\r\n", "1\t75959\t75961\t0.000000\r\n", "1\t75962\t75964\t0.000000\r\n", "1\t75993\t75995\t0.000000\r\n", "1\t75996\t75998\t0.000000\r\n", "\r\n", "==> Meth11_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-mcGenes <==\r\n", "1\t58745\t58747\t100.000000\r\n", "1\t59207\t59209\t100.000000\r\n", "1\t69235\t69237\t100.000000\r\n", "1\t69271\t69273\t80.000000\r\n", "1\t69275\t69277\t100.000000\r\n", "1\t69451\t69453\t100.000000\r\n", "1\t69580\t69582\t100.000000\r\n", "1\t69584\t69586\t100.000000\r\n", "1\t69845\t69847\t100.000000\r\n", "1\t69983\t69985\t100.000000\r\n", "\r\n", "==> Meth11_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-mcGenes <==\r\n", "1\t74928\t74930\t14.285714\r\n", "1\t238262\t238264\t11.111111\r\n", "1\t324573\t324575\t16.666667\r\n", "1\t325051\t325053\t16.666667\r\n", "1\t325110\t325112\t20.000000\r\n", "1\t331130\t331132\t11.111111\r\n", "1\t334055\t334057\t20.000000\r\n", "1\t334782\t334784\t28.571429\r\n", "1\t334792\t334794\t16.666667\r\n", "1\t334973\t334975\t40.000000\r\n", "\r\n", "==> Meth11_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-mcGenes <==\r\n", "1\t75182\t75184\t0.000000\r\n", "1\t75306\t75308\t0.000000\r\n", "1\t75959\t75961\t0.000000\r\n", "1\t75962\t75964\t0.000000\r\n", "1\t75993\t75995\t0.000000\r\n", "1\t75996\t75998\t0.000000\r\n", "1\t76020\t76022\t0.000000\r\n", "1\t77745\t77747\t0.000000\r\n", "1\t77838\t77840\t0.000000\r\n", "1\t77846\t77848\t0.000000\r\n", "\r\n", "==> Meth11_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-mcGenes <==\r\n", "1\t58745\t58747\t100.000000\r\n", "1\t59207\t59209\t100.000000\r\n", "1\t69235\t69237\t100.000000\r\n", "1\t69271\t69273\t80.000000\r\n", "1\t69275\t69277\t100.000000\r\n", "1\t69451\t69453\t100.000000\r\n", "1\t69580\t69582\t100.000000\r\n", "1\t69584\t69586\t100.000000\r\n", "1\t69845\t69847\t100.000000\r\n", "1\t69983\t69985\t100.000000\r\n", "\r\n", "==> Meth12_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-mcGenes <==\r\n", "1\t58609\t58611\t100.000000\r\n", "1\t58618\t58620\t100.000000\r\n", "1\t59207\t59209\t100.000000\r\n", "1\t59277\t59279\t100.000000\r\n", "1\t59393\t59395\t100.000000\r\n", "1\t59438\t59440\t100.000000\r\n", "1\t65972\t65974\t100.000000\r\n", "1\t65978\t65980\t100.000000\r\n", "1\t66345\t66347\t100.000000\r\n", "1\t66354\t66356\t100.000000\r\n", "\r\n", "==> Meth12_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-mcGenes <==\r\n", "1\t23202\t23204\t12.500000\r\n", "1\t23382\t23384\t33.333333\r\n", "1\t23425\t23427\t20.000000\r\n", "1\t42323\t42325\t20.000000\r\n", "1\t45844\t45846\t28.571429\r\n", "1\t45913\t45915\t12.500000\r\n", "1\t45949\t45951\t12.500000\r\n", "1\t46485\t46487\t12.500000\r\n", "1\t48831\t48833\t20.000000\r\n", "1\t48881\t48883\t20.000000\r\n", "\r\n", "==> Meth12_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-mcGenes <==\r\n", "1\t23003\t23005\t0.000000\r\n", "1\t23006\t23008\t0.000000\r\n", "1\t23019\t23021\t0.000000\r\n", "1\t23139\t23141\t0.000000\r\n", "1\t23173\t23175\t0.000000\r\n", "1\t23326\t23328\t0.000000\r\n", "1\t23334\t23336\t0.000000\r\n", "1\t23404\t23406\t0.000000\r\n", "1\t23445\t23447\t0.000000\r\n", "1\t37555\t37557\t0.000000\r\n", "\r\n", "==> Meth12_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-mcGenes <==\r\n", "1\t23003\t23005\t0.000000\r\n", "1\t23006\t23008\t0.000000\r\n", "1\t23019\t23021\t0.000000\r\n", "1\t23139\t23141\t0.000000\r\n", "1\t23173\t23175\t0.000000\r\n", "1\t23202\t23204\t12.500000\r\n", "1\t23326\t23328\t0.000000\r\n", "1\t23334\t23336\t0.000000\r\n", "1\t23382\t23384\t33.333333\r\n", "1\t23404\t23406\t0.000000\r\n", "\r\n", "==> Meth13_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-mcGenes <==\r\n", "1\t58618\t58620\t100.000000\r\n", "1\t58745\t58747\t97.959184\r\n", "1\t58764\t58766\t100.000000\r\n", "1\t58792\t58794\t92.592593\r\n", "1\t66041\t66043\t100.000000\r\n", "1\t66050\t66052\t100.000000\r\n", "1\t66339\t66341\t88.888889\r\n", "1\t66345\t66347\t77.777778\r\n", "1\t66354\t66356\t77.777778\r\n", "1\t66400\t66402\t100.000000\r\n", "\r\n", "==> Meth13_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-mcGenes <==\r\n", "1\t45163\t45165\t10.317460\r\n", "1\t48370\t48372\t14.285714\r\n", "1\t89011\t89013\t14.285714\r\n", "1\t332927\t332929\t25.000000\r\n", "1\t336069\t336071\t28.342246\r\n", "1\t336217\t336219\t33.673469\r\n", "1\t349633\t349635\t13.978495\r\n", "1\t369283\t369285\t10.638298\r\n", "1\t369679\t369681\t11.688312\r\n", "1\t372648\t372650\t18.750000\r\n", "\r\n", "==> Meth13_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-mcGenes <==\r\n", "1\t22445\t22447\t0.000000\r\n", "1\t22505\t22507\t0.000000\r\n", "1\t22513\t22515\t0.000000\r\n", "1\t22531\t22533\t0.000000\r\n", "1\t22534\t22536\t0.000000\r\n", "1\t22547\t22549\t0.000000\r\n", "1\t22563\t22565\t0.000000\r\n", "1\t22575\t22577\t0.000000\r\n", "1\t23117\t23119\t0.000000\r\n", "1\t23139\t23141\t0.000000\r\n", "\r\n", "==> Meth13_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-mcGenes <==\r\n", "1\t22445\t22447\t0.000000\r\n", "1\t22505\t22507\t0.000000\r\n", "1\t22513\t22515\t0.000000\r\n", "1\t22531\t22533\t0.000000\r\n", "1\t22534\t22536\t0.000000\r\n", "1\t22547\t22549\t0.000000\r\n", "1\t22563\t22565\t0.000000\r\n", "1\t22575\t22577\t0.000000\r\n", "1\t23117\t23119\t0.000000\r\n", "1\t23139\t23141\t0.000000\r\n", "\r\n", "==> Meth14_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-mcGenes <==\r\n", "1\t58618\t58620\t94.117647\r\n", "1\t58745\t58747\t100.000000\r\n", "1\t58764\t58766\t100.000000\r\n", "1\t58792\t58794\t100.000000\r\n", "1\t105822\t105824\t100.000000\r\n", "1\t105825\t105827\t100.000000\r\n", "1\t105836\t105838\t100.000000\r\n", "1\t105874\t105876\t100.000000\r\n", "1\t105883\t105885\t87.500000\r\n", "1\t105953\t105955\t50.000000\r\n", "\r\n", "==> Meth14_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-mcGenes <==\r\n", "1\t124833\t124835\t20.000000\r\n", "1\t135853\t135855\t33.333333\r\n", "1\t323888\t323890\t10.526316\r\n", "1\t336069\t336071\t13.385827\r\n", "1\t344217\t344219\t11.846690\r\n", "1\t349633\t349635\t11.764706\r\n", "1\t367234\t367236\t11.486486\r\n", "1\t484816\t484818\t13.709677\r\n", "1\t527706\t527708\t23.469388\r\n", "1\t527726\t527728\t14.659686\r\n", "\r\n", "==> Meth14_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-mcGenes <==\r\n", "1\t40450\t40452\t0.000000\r\n", "1\t40486\t40488\t0.000000\r\n", "1\t40541\t40543\t0.000000\r\n", "1\t40552\t40554\t0.000000\r\n", "1\t40555\t40557\t0.000000\r\n", "1\t42285\t42287\t0.000000\r\n", "1\t42304\t42306\t0.000000\r\n", "1\t42313\t42315\t0.000000\r\n", "1\t42323\t42325\t0.000000\r\n", "1\t42327\t42329\t0.000000\r\n", "\r\n", "==> Meth14_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-mcGenes <==\r\n", "1\t40450\t40452\t0.000000\r\n", "1\t40486\t40488\t0.000000\r\n", "1\t40541\t40543\t0.000000\r\n", "1\t40552\t40554\t0.000000\r\n", "1\t40555\t40557\t0.000000\r\n", "1\t42285\t42287\t0.000000\r\n", "1\t42304\t42306\t0.000000\r\n", "1\t42313\t42315\t0.000000\r\n", "1\t42323\t42325\t0.000000\r\n", "1\t42327\t42329\t0.000000\r\n", "\r\n", "==> Meth15_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-mcGenes <==\r\n", "1\t58618\t58620\t92.857143\r\n", "1\t58745\t58747\t92.500000\r\n", "1\t58764\t58766\t97.500000\r\n", "1\t58792\t58794\t57.692308\r\n", "1\t101462\t101464\t90.476190\r\n", "1\t101535\t101537\t100.000000\r\n", "1\t108751\t108753\t100.000000\r\n", "1\t108778\t108780\t100.000000\r\n", "1\t108787\t108789\t82.758621\r\n", "1\t108803\t108805\t100.000000\r\n", "\r\n", "==> Meth15_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-mcGenes <==\r\n", "1\t41916\t41918\t13.043478\r\n", "1\t42261\t42263\t16.666667\r\n", "1\t78269\t78271\t22.222222\r\n", "1\t101503\t101505\t31.428571\r\n", "1\t101545\t101547\t40.000000\r\n", "1\t186492\t186494\t11.111111\r\n", "1\t237958\t237960\t28.571429\r\n", "1\t332804\t332806\t11.764706\r\n", "1\t336069\t336071\t20.496894\r\n", "1\t336217\t336219\t36.666667\r\n", "\r\n", "==> Meth15_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-mcGenes <==\r\n", "1\t40450\t40452\t2.816901\r\n", "1\t40486\t40488\t0.000000\r\n", "1\t40541\t40543\t0.826446\r\n", "1\t40552\t40554\t0.000000\r\n", "1\t40555\t40557\t9.803922\r\n", "1\t41832\t41834\t0.000000\r\n", "1\t41845\t41847\t0.000000\r\n", "1\t41864\t41866\t0.000000\r\n", "1\t41974\t41976\t0.000000\r\n", "1\t42117\t42119\t4.347826\r\n", "\r\n", "==> Meth15_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-mcGenes <==\r\n", "1\t40450\t40452\t2.816901\r\n", "1\t40486\t40488\t0.000000\r\n", "1\t40541\t40543\t0.826446\r\n", "1\t40552\t40554\t0.000000\r\n", "1\t40555\t40557\t9.803922\r\n", "1\t41832\t41834\t0.000000\r\n", "1\t41845\t41847\t0.000000\r\n", "1\t41864\t41866\t0.000000\r\n", "1\t41916\t41918\t13.043478\r\n", "1\t41974\t41976\t0.000000\r\n", "\r\n", "==> Meth16_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-mcGenes <==\r\n", "1\t344031\t344033\t50.000000\r\n", "1\t344044\t344046\t60.000000\r\n", "1\t786125\t786127\t60.000000\r\n", "1\t786144\t786146\t100.000000\r\n", "1\t786151\t786153\t100.000000\r\n", "1\t879915\t879917\t100.000000\r\n", "1\t883893\t883895\t50.000000\r\n", "1\t982886\t982888\t60.000000\r\n", "1\t1259506\t1259508\t100.000000\r\n", "1\t1259529\t1259531\t100.000000\r\n", "\r\n", "==> Meth16_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-mcGenes <==\r\n", "1\t323095\t323097\t16.666667\r\n", "1\t328382\t328384\t20.000000\r\n", "1\t328386\t328388\t20.000000\r\n", "1\t330194\t330196\t20.000000\r\n", "1\t330197\t330199\t20.000000\r\n", "1\t334750\t334752\t14.285714\r\n", "1\t334782\t334784\t14.285714\r\n", "1\t341742\t341744\t20.000000\r\n", "1\t343939\t343941\t28.571429\r\n", "1\t343962\t343964\t42.857143\r\n", "\r\n", "==> Meth16_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-mcGenes <==\r\n", "1\t77096\t77098\t0.000000\r\n", "1\t77145\t77147\t0.000000\r\n", "1\t77151\t77153\t0.000000\r\n", "1\t77179\t77181\t0.000000\r\n", "1\t81812\t81814\t0.000000\r\n", "1\t81817\t81819\t0.000000\r\n", "1\t81835\t81837\t0.000000\r\n", "1\t81874\t81876\t0.000000\r\n", "1\t81887\t81889\t0.000000\r\n", "1\t109670\t109672\t0.000000\r\n", "\r\n", "==> Meth16_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-mcGenes <==\r\n", "1\t77096\t77098\t0.000000\r\n", "1\t77145\t77147\t0.000000\r\n", "1\t77151\t77153\t0.000000\r\n", "1\t77179\t77181\t0.000000\r\n", "1\t81812\t81814\t0.000000\r\n", "1\t81817\t81819\t0.000000\r\n", "1\t81835\t81837\t0.000000\r\n", "1\t81874\t81876\t0.000000\r\n", "1\t81887\t81889\t0.000000\r\n", "1\t109670\t109672\t0.000000\r\n", "\r\n", "==> Meth17_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-mcGenes <==\r\n", "1\t59438\t59440\t100.000000\r\n", "1\t106173\t106175\t100.000000\r\n", "1\t106202\t106204\t100.000000\r\n", "1\t1243019\t1243021\t60.000000\r\n", "1\t1409734\t1409736\t100.000000\r\n", "1\t1419093\t1419095\t87.500000\r\n", "1\t1457412\t1457414\t100.000000\r\n", "1\t1457444\t1457446\t80.000000\r\n", "1\t1457447\t1457449\t100.000000\r\n", "1\t1457450\t1457452\t100.000000\r\n", "\r\n", "==> Meth17_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-mcGenes <==\r\n", "1\t601511\t601513\t20.000000\r\n", "1\t666749\t666751\t16.666667\r\n", "1\t709103\t709105\t20.000000\r\n", "1\t744333\t744335\t25.000000\r\n", "1\t744365\t744367\t11.111111\r\n", "1\t884009\t884011\t20.000000\r\n", "1\t890256\t890258\t28.571429\r\n", "1\t890269\t890271\t14.285714\r\n", "1\t1123450\t1123452\t20.000000\r\n", "1\t1125135\t1125137\t20.000000\r\n", "\r\n", "==> Meth17_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-mcGenes <==\r\n", "1\t324616\t324618\t0.000000\r\n", "1\t336227\t336229\t0.000000\r\n", "1\t336251\t336253\t0.000000\r\n", "1\t336289\t336291\t0.000000\r\n", "1\t336307\t336309\t0.000000\r\n", "1\t336371\t336373\t0.000000\r\n", "1\t336396\t336398\t0.000000\r\n", "1\t336403\t336405\t0.000000\r\n", "1\t336423\t336425\t0.000000\r\n", "1\t336427\t336429\t0.000000\r\n", "\r\n", "==> Meth17_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-mcGenes <==\r\n", "1\t59438\t59440\t100.000000\r\n", "1\t106173\t106175\t100.000000\r\n", "1\t106202\t106204\t100.000000\r\n", "1\t324616\t324618\t0.000000\r\n", "1\t336227\t336229\t0.000000\r\n", "1\t336251\t336253\t0.000000\r\n", "1\t336289\t336291\t0.000000\r\n", "1\t336307\t336309\t0.000000\r\n", "1\t336371\t336373\t0.000000\r\n", "1\t336396\t336398\t0.000000\r\n", "\r\n", "==> Meth18_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-mcGenes <==\r\n", "1\t1468323\t1468325\t100.000000\r\n", "1\t1468670\t1468672\t100.000000\r\n", "1\t1468680\t1468682\t100.000000\r\n", "1\t1468683\t1468685\t100.000000\r\n", "1\t1468693\t1468695\t100.000000\r\n", "1\t1468700\t1468702\t100.000000\r\n", "1\t1468710\t1468712\t100.000000\r\n", "1\t1468737\t1468739\t100.000000\r\n", "1\t1468744\t1468746\t100.000000\r\n", "1\t1468749\t1468751\t100.000000\r\n", "\r\n", "==> Meth18_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-mcGenes <==\r\n", "1\t480696\t480698\t20.000000\r\n", "1\t667790\t667792\t40.000000\r\n", "1\t889205\t889207\t20.000000\r\n", "1\t906918\t906920\t20.000000\r\n", "1\t906936\t906938\t16.666667\r\n", "1\t1045868\t1045870\t20.000000\r\n", "1\t1045903\t1045905\t20.000000\r\n", "1\t1046004\t1046006\t20.000000\r\n", "1\t1131883\t1131885\t20.000000\r\n", "1\t1131892\t1131894\t20.000000\r\n", "\r\n", "==> Meth18_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-mcGenes <==\r\n", "1\t324315\t324317\t0.000000\r\n", "1\t324332\t324334\t0.000000\r\n", "1\t324348\t324350\t0.000000\r\n", "1\t324368\t324370\t0.000000\r\n", "1\t324424\t324426\t0.000000\r\n", "1\t354586\t354588\t0.000000\r\n", "1\t374059\t374061\t0.000000\r\n", "1\t374080\t374082\t0.000000\r\n", "1\t401787\t401789\t0.000000\r\n", "1\t435464\t435466\t0.000000\r\n", "\r\n", "==> Meth18_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-mcGenes <==\r\n", "1\t324315\t324317\t0.000000\r\n", "1\t324332\t324334\t0.000000\r\n", "1\t324348\t324350\t0.000000\r\n", "1\t324368\t324370\t0.000000\r\n", "1\t324424\t324426\t0.000000\r\n", "1\t354586\t354588\t0.000000\r\n", "1\t374059\t374061\t0.000000\r\n", "1\t374080\t374082\t0.000000\r\n", "1\t401787\t401789\t0.000000\r\n", "1\t435464\t435466\t0.000000\r\n" ] } ], "source": [ "#Check output\n", "!head *mcGenes" ] }, { "cell_type": "code", "execution_count": 117, "metadata": { "collapsed": false, "scrolled": true }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ " 299552 Meth10_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-mcGenes\n", " 256905 Meth10_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-mcGenes\n", " 1622564 Meth10_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-mcGenes\n", " 2179021 Meth10_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-mcGenes\n", " 348165 Meth11_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-mcGenes\n", " 247314 Meth11_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-mcGenes\n", " 1657052 Meth11_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-mcGenes\n", " 2252531 Meth11_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-mcGenes\n", " 690220 Meth12_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-mcGenes\n", " 457862 Meth12_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-mcGenes\n", " 3021017 Meth12_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-mcGenes\n", " 4169099 Meth12_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-mcGenes\n", " 158655 Meth13_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-mcGenes\n", " 69764 Meth13_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-mcGenes\n", " 1157398 Meth13_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-mcGenes\n", " 1385817 Meth13_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-mcGenes\n", " 114687 Meth14_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-mcGenes\n", " 63579 Meth14_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-mcGenes\n", " 982662 Meth14_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-mcGenes\n", " 1160928 Meth14_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-mcGenes\n", " 144825 Meth15_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-mcGenes\n", " 83339 Meth15_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-mcGenes\n", " 1154282 Meth15_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-mcGenes\n", " 1382446 Meth15_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-mcGenes\n", " 63836 Meth16_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-mcGenes\n", " 33282 Meth16_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-mcGenes\n", " 175254 Meth16_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-mcGenes\n", " 272372 Meth16_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-mcGenes\n", " 26915 Meth17_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-mcGenes\n", " 12314 Meth17_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-mcGenes\n", " 69251 Meth17_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-mcGenes\n", " 108480 Meth17_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-mcGenes\n", " 16697 Meth18_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-mcGenes\n", " 6471 Meth18_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-mcGenes\n", " 42916 Meth18_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-mcGenes\n", " 66084 Meth18_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-mcGenes\n", " 25953556 total\n" ] } ], "source": [ "#Count number of overlaps\n", "!wc -l *mcGenes" ] }, { "cell_type": "code", "execution_count": 118, "metadata": { "collapsed": true }, "outputs": [], "source": [ "!wc -l *mcGenes > Mcap-5x-mcGenes-counts.txt" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "#### 4c. Coding Sequences (CDS)" ] }, { "cell_type": "code", "execution_count": 119, "metadata": { "collapsed": true, "scrolled": true }, "outputs": [], "source": [ "%%bash\n", "\n", "for f in *bed\n", "do\n", " /usr/local/bin/intersectBed \\\n", " -u \\\n", " -a ${f} \\\n", " -b ../../../genome-feature-files/Mcap.GFFannotation.CDS.gff \\\n", " > ${f}-mcCDS\n", "done" ] }, { "cell_type": "code", "execution_count": 120, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "==> Meth10_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-mcCDS <==\r\n", "1\t58745\t58747\t100.000000\r\n", "1\t438779\t438781\t100.000000\r\n", "1\t438791\t438793\t100.000000\r\n", "1\t786125\t786127\t50.000000\r\n", "1\t786144\t786146\t50.000000\r\n", "1\t789544\t789546\t50.000000\r\n", "1\t789590\t789592\t50.000000\r\n", "1\t879226\t879228\t100.000000\r\n", "1\t983540\t983542\t100.000000\r\n", "1\t1263116\t1263118\t100.000000\r\n", "\r\n", "==> Meth10_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-mcCDS <==\r\n", "1\t184266\t184268\t16.666667\r\n", "1\t184271\t184273\t16.666667\r\n", "1\t238091\t238093\t12.500000\r\n", "1\t307885\t307887\t20.000000\r\n", "1\t345002\t345004\t12.500000\r\n", "1\t349163\t349165\t22.222222\r\n", "1\t356955\t356957\t20.000000\r\n", "1\t401872\t401874\t14.285714\r\n", "1\t401879\t401881\t12.500000\r\n", "1\t402084\t402086\t12.500000\r\n", "\r\n", "==> Meth10_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-mcCDS <==\r\n", "1\t75959\t75961\t0.000000\r\n", "1\t75962\t75964\t0.000000\r\n", "1\t75993\t75995\t0.000000\r\n", "1\t75996\t75998\t0.000000\r\n", "1\t80478\t80480\t0.000000\r\n", "1\t109952\t109954\t0.000000\r\n", "1\t109984\t109986\t0.000000\r\n", "1\t133020\t133022\t0.000000\r\n", "1\t133022\t133024\t0.000000\r\n", "1\t133024\t133026\t0.000000\r\n", "\r\n", "==> Meth10_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-mcCDS <==\r\n", "1\t58745\t58747\t100.000000\r\n", "1\t75959\t75961\t0.000000\r\n", "1\t75962\t75964\t0.000000\r\n", "1\t75993\t75995\t0.000000\r\n", "1\t75996\t75998\t0.000000\r\n", "1\t80478\t80480\t0.000000\r\n", "1\t109952\t109954\t0.000000\r\n", "1\t109984\t109986\t0.000000\r\n", "1\t133020\t133022\t0.000000\r\n", "1\t133022\t133024\t0.000000\r\n", "\r\n", "==> Meth11_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-mcCDS <==\r\n", "1\t58745\t58747\t100.000000\r\n", "1\t59207\t59209\t100.000000\r\n", "1\t437346\t437348\t50.000000\r\n", "1\t443146\t443148\t66.666667\r\n", "1\t443240\t443242\t83.333333\r\n", "1\t443243\t443245\t83.333333\r\n", "1\t443255\t443257\t83.333333\r\n", "1\t443278\t443280\t80.000000\r\n", "1\t744619\t744621\t54.545455\r\n", "1\t786144\t786146\t55.555556\r\n", "\r\n", "==> Meth11_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-mcCDS <==\r\n", "1\t238262\t238264\t11.111111\r\n", "1\t340943\t340945\t20.000000\r\n", "1\t349188\t349190\t16.666667\r\n", "1\t354622\t354624\t16.666667\r\n", "1\t361866\t361868\t20.000000\r\n", "1\t401952\t401954\t11.111111\r\n", "1\t401999\t402001\t12.500000\r\n", "1\t402034\t402036\t16.666667\r\n", "1\t402060\t402062\t16.666667\r\n", "1\t402183\t402185\t14.285714\r\n", "\r\n", "==> Meth11_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-mcCDS <==\r\n", "1\t75959\t75961\t0.000000\r\n", "1\t75962\t75964\t0.000000\r\n", "1\t75993\t75995\t0.000000\r\n", "1\t75996\t75998\t0.000000\r\n", "1\t76020\t76022\t0.000000\r\n", "1\t218048\t218050\t0.000000\r\n", "1\t218050\t218052\t0.000000\r\n", "1\t218054\t218056\t0.000000\r\n", "1\t218107\t218109\t0.000000\r\n", "1\t218110\t218112\t0.000000\r\n", "\r\n", "==> Meth11_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-mcCDS <==\r\n", "1\t58745\t58747\t100.000000\r\n", "1\t59207\t59209\t100.000000\r\n", "1\t75959\t75961\t0.000000\r\n", "1\t75962\t75964\t0.000000\r\n", "1\t75993\t75995\t0.000000\r\n", "1\t75996\t75998\t0.000000\r\n", "1\t76020\t76022\t0.000000\r\n", "1\t218048\t218050\t0.000000\r\n", "1\t218050\t218052\t0.000000\r\n", "1\t218054\t218056\t0.000000\r\n", "\r\n", "==> Meth12_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-mcCDS <==\r\n", "1\t58609\t58611\t100.000000\r\n", "1\t58618\t58620\t100.000000\r\n", "1\t59207\t59209\t100.000000\r\n", "1\t59277\t59279\t100.000000\r\n", "1\t59393\t59395\t100.000000\r\n", "1\t59438\t59440\t100.000000\r\n", "1\t104744\t104746\t100.000000\r\n", "1\t351074\t351076\t85.714286\r\n", "1\t351086\t351088\t77.777778\r\n", "1\t438930\t438932\t50.000000\r\n", "\r\n", "==> Meth12_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-mcCDS <==\r\n", "1\t80301\t80303\t20.000000\r\n", "1\t80430\t80432\t20.000000\r\n", "1\t82663\t82665\t20.000000\r\n", "1\t238091\t238093\t12.500000\r\n", "1\t238280\t238282\t20.000000\r\n", "1\t331583\t331585\t16.666667\r\n", "1\t332411\t332413\t14.285714\r\n", "1\t332445\t332447\t16.666667\r\n", "1\t356913\t356915\t14.285714\r\n", "1\t361980\t361982\t14.285714\r\n", "\r\n", "==> Meth12_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-mcCDS <==\r\n", "1\t37555\t37557\t0.000000\r\n", "1\t37567\t37569\t0.000000\r\n", "1\t45110\t45112\t0.000000\r\n", "1\t45116\t45118\t0.000000\r\n", "1\t45128\t45130\t0.000000\r\n", "1\t45199\t45201\t0.000000\r\n", "1\t46633\t46635\t0.000000\r\n", "1\t46642\t46644\t0.000000\r\n", "1\t46648\t46650\t0.000000\r\n", "1\t51924\t51926\t0.000000\r\n", "\r\n", "==> Meth12_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-mcCDS <==\r\n", "1\t37555\t37557\t0.000000\r\n", "1\t37567\t37569\t0.000000\r\n", "1\t45110\t45112\t0.000000\r\n", "1\t45116\t45118\t0.000000\r\n", "1\t45128\t45130\t0.000000\r\n", "1\t45199\t45201\t0.000000\r\n", "1\t46633\t46635\t0.000000\r\n", "1\t46642\t46644\t0.000000\r\n", "1\t46648\t46650\t0.000000\r\n", "1\t51924\t51926\t0.000000\r\n", "\r\n", "==> Meth13_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-mcCDS <==\r\n", "1\t58618\t58620\t100.000000\r\n", "1\t58745\t58747\t97.959184\r\n", "1\t58764\t58766\t100.000000\r\n", "1\t58792\t58794\t92.592593\r\n", "1\t1367668\t1367670\t96.610169\r\n", "1\t1641547\t1641549\t87.500000\r\n", "1\t1641670\t1641672\t96.969697\r\n", "1\t1641723\t1641725\t100.000000\r\n", "1\t1677775\t1677777\t60.714286\r\n", "1\t1750014\t1750016\t92.592593\r\n", "\r\n", "==> Meth13_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-mcCDS <==\r\n", "1\t45163\t45165\t10.317460\r\n", "1\t491140\t491142\t10.638298\r\n", "1\t526047\t526049\t11.764706\r\n", "1\t607861\t607863\t13.157895\r\n", "1\t894945\t894947\t10.958904\r\n", "1\t940040\t940042\t16.455696\r\n", "1\t960189\t960191\t10.948905\r\n", "1\t1130680\t1130682\t11.111111\r\n", "1\t1587400\t1587402\t11.111111\r\n", "1\t1677795\t1677797\t25.000000\r\n", "\r\n", "==> Meth13_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-mcCDS <==\r\n", "1\t22445\t22447\t0.000000\r\n", "1\t22505\t22507\t0.000000\r\n", "1\t22513\t22515\t0.000000\r\n", "1\t22531\t22533\t0.000000\r\n", "1\t22534\t22536\t0.000000\r\n", "1\t22547\t22549\t0.000000\r\n", "1\t22563\t22565\t0.000000\r\n", "1\t22575\t22577\t0.000000\r\n", "1\t45046\t45048\t0.000000\r\n", "1\t45070\t45072\t0.591716\r\n", "\r\n", "==> Meth13_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-mcCDS <==\r\n", "1\t22445\t22447\t0.000000\r\n", "1\t22505\t22507\t0.000000\r\n", "1\t22513\t22515\t0.000000\r\n", "1\t22531\t22533\t0.000000\r\n", "1\t22534\t22536\t0.000000\r\n", "1\t22547\t22549\t0.000000\r\n", "1\t22563\t22565\t0.000000\r\n", "1\t22575\t22577\t0.000000\r\n", "1\t45046\t45048\t0.000000\r\n", "1\t45070\t45072\t0.591716\r\n", "\r\n", "==> Meth14_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-mcCDS <==\r\n", "1\t58618\t58620\t94.117647\r\n", "1\t58745\t58747\t100.000000\r\n", "1\t58764\t58766\t100.000000\r\n", "1\t58792\t58794\t100.000000\r\n", "1\t1367668\t1367670\t94.736842\r\n", "1\t1750088\t1750090\t100.000000\r\n", "1\t1869676\t1869678\t80.327869\r\n", "1\t2136506\t2136508\t100.000000\r\n", "1\t2518245\t2518247\t100.000000\r\n", "1\t3027422\t3027424\t100.000000\r\n", "\r\n", "==> Meth14_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-mcCDS <==\r\n", "1\t587749\t587751\t10.416667\r\n", "1\t743735\t743737\t28.888889\r\n", "1\t743825\t743827\t20.000000\r\n", "1\t744333\t744335\t21.739130\r\n", "1\t744680\t744682\t23.076923\r\n", "1\t785550\t785552\t25.000000\r\n", "1\t785779\t785781\t10.666667\r\n", "1\t946097\t946099\t16.666667\r\n", "1\t961234\t961236\t11.764706\r\n", "1\t1020443\t1020445\t15.000000\r\n", "\r\n", "==> Meth14_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-mcCDS <==\r\n", "1\t45046\t45048\t0.000000\r\n", "1\t45070\t45072\t3.773585\r\n", "1\t45110\t45112\t0.000000\r\n", "1\t45116\t45118\t0.000000\r\n", "1\t45128\t45130\t0.000000\r\n", "1\t45154\t45156\t0.000000\r\n", "1\t349163\t349165\t0.000000\r\n", "1\t349182\t349184\t0.000000\r\n", "1\t349188\t349190\t0.000000\r\n", "1\t349242\t349244\t0.000000\r\n", "\r\n", "==> Meth14_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-mcCDS <==\r\n", "1\t45046\t45048\t0.000000\r\n", "1\t45070\t45072\t3.773585\r\n", "1\t45110\t45112\t0.000000\r\n", "1\t45116\t45118\t0.000000\r\n", "1\t45128\t45130\t0.000000\r\n", "1\t45154\t45156\t0.000000\r\n", "1\t58618\t58620\t94.117647\r\n", "1\t58745\t58747\t100.000000\r\n", "1\t58764\t58766\t100.000000\r\n", "1\t58792\t58794\t100.000000\r\n", "\r\n", "==> Meth15_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-mcCDS <==\r\n", "1\t58618\t58620\t92.857143\r\n", "1\t58745\t58747\t92.500000\r\n", "1\t58764\t58766\t97.500000\r\n", "1\t58792\t58794\t57.692308\r\n", "1\t1174296\t1174298\t50.000000\r\n", "1\t1432386\t1432388\t66.666667\r\n", "1\t1432398\t1432400\t66.666667\r\n", "1\t1432427\t1432429\t66.666667\r\n", "1\t1432441\t1432443\t66.666667\r\n", "1\t1641547\t1641549\t100.000000\r\n", "\r\n", "==> Meth15_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-mcCDS <==\r\n", "1\t186492\t186494\t11.111111\r\n", "1\t237958\t237960\t28.571429\r\n", "1\t491140\t491142\t11.111111\r\n", "1\t587667\t587669\t10.156250\r\n", "1\t608281\t608283\t14.285714\r\n", "1\t708875\t708877\t20.000000\r\n", "1\t946097\t946099\t15.384615\r\n", "1\t1064399\t1064401\t13.043478\r\n", "1\t1134015\t1134017\t16.666667\r\n", "1\t1174115\t1174117\t12.359551\r\n", "\r\n", "==> Meth15_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-mcCDS <==\r\n", "1\t148380\t148382\t5.000000\r\n", "1\t148390\t148392\t0.000000\r\n", "1\t148392\t148394\t0.000000\r\n", "1\t148396\t148398\t0.000000\r\n", "1\t148406\t148408\t0.000000\r\n", "1\t148429\t148431\t0.000000\r\n", "1\t148451\t148453\t0.000000\r\n", "1\t148455\t148457\t0.000000\r\n", "1\t148457\t148459\t0.000000\r\n", "1\t148462\t148464\t0.000000\r\n", "\r\n", "==> Meth15_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-mcCDS <==\r\n", "1\t58618\t58620\t92.857143\r\n", "1\t58745\t58747\t92.500000\r\n", "1\t58764\t58766\t97.500000\r\n", "1\t58792\t58794\t57.692308\r\n", "1\t148380\t148382\t5.000000\r\n", "1\t148390\t148392\t0.000000\r\n", "1\t148392\t148394\t0.000000\r\n", "1\t148396\t148398\t0.000000\r\n", "1\t148406\t148408\t0.000000\r\n", "1\t148429\t148431\t0.000000\r\n", "\r\n", "==> Meth16_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-mcCDS <==\r\n", "1\t786125\t786127\t60.000000\r\n", "1\t786144\t786146\t100.000000\r\n", "1\t786151\t786153\t100.000000\r\n", "1\t1263040\t1263042\t100.000000\r\n", "1\t1409642\t1409644\t100.000000\r\n", "1\t1409734\t1409736\t100.000000\r\n", "1\t1543924\t1543926\t100.000000\r\n", "1\t1601051\t1601053\t100.000000\r\n", "1\t1641103\t1641105\t100.000000\r\n", "1\t1643341\t1643343\t100.000000\r\n", "\r\n", "==> Meth16_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-mcCDS <==\r\n", "1\t323095\t323097\t16.666667\r\n", "1\t354622\t354624\t20.000000\r\n", "1\t786094\t786096\t33.333333\r\n", "1\t786097\t786099\t16.666667\r\n", "1\t789648\t789650\t28.571429\r\n", "1\t789673\t789675\t28.571429\r\n", "1\t789690\t789692\t33.333333\r\n", "1\t789693\t789695\t33.333333\r\n", "1\t903036\t903038\t20.000000\r\n", "1\t1176328\t1176330\t20.000000\r\n", "\r\n", "==> Meth16_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-mcCDS <==\r\n", "1\t109670\t109672\t0.000000\r\n", "1\t238112\t238114\t0.000000\r\n", "1\t238133\t238135\t0.000000\r\n", "1\t323036\t323038\t0.000000\r\n", "1\t323051\t323053\t0.000000\r\n", "1\t323066\t323068\t0.000000\r\n", "1\t323098\t323100\t0.000000\r\n", "1\t354616\t354618\t0.000000\r\n", "1\t361975\t361977\t0.000000\r\n", "1\t361980\t361982\t0.000000\r\n", "\r\n", "==> Meth16_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-mcCDS <==\r\n", "1\t109670\t109672\t0.000000\r\n", "1\t238112\t238114\t0.000000\r\n", "1\t238133\t238135\t0.000000\r\n", "1\t323036\t323038\t0.000000\r\n", "1\t323051\t323053\t0.000000\r\n", "1\t323066\t323068\t0.000000\r\n", "1\t323095\t323097\t16.666667\r\n", "1\t323098\t323100\t0.000000\r\n", "1\t354616\t354618\t0.000000\r\n", "1\t354622\t354624\t20.000000\r\n", "\r\n", "==> Meth17_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-mcCDS <==\r\n", "1\t59438\t59440\t100.000000\r\n", "1\t1409734\t1409736\t100.000000\r\n", "1\t2018373\t2018375\t100.000000\r\n", "1\t2531489\t2531491\t50.000000\r\n", "2\t1984186\t1984188\t60.000000\r\n", "2\t1984196\t1984198\t60.000000\r\n", "2\t1984257\t1984259\t50.000000\r\n", "2\t1984273\t1984275\t60.000000\r\n", "2\t2316591\t2316593\t80.000000\r\n", "2\t2610818\t2610820\t100.000000\r\n", "\r\n", "==> Meth17_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-mcCDS <==\r\n", "1\t601511\t601513\t20.000000\r", "\r\n", "1\t666749\t666751\t16.666667\r\n", "1\t709103\t709105\t20.000000\r\n", "1\t744333\t744335\t25.000000\r\n", "1\t744365\t744367\t11.111111\r\n", "1\t1174872\t1174874\t33.333333\r\n", "1\t1174927\t1174929\t28.571429\r\n", "1\t1174940\t1174942\t25.000000\r\n", "1\t1174950\t1174952\t16.666667\r\n", "1\t1561745\t1561747\t20.000000\r\n", "\r\n", "==> Meth17_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-mcCDS <==\r\n", "1\t363057\t363059\t0.000000\r\n", "1\t363078\t363080\t0.000000\r\n", "1\t363110\t363112\t0.000000\r\n", "1\t435752\t435754\t0.000000\r\n", "1\t525493\t525495\t0.000000\r\n", "1\t525498\t525500\t0.000000\r\n", "1\t525538\t525540\t0.000000\r\n", "1\t525578\t525580\t0.000000\r\n", "1\t525620\t525622\t0.000000\r\n", "1\t525647\t525649\t0.000000\r\n", "\r\n", "==> Meth17_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-mcCDS <==\r\n", "1\t59438\t59440\t100.000000\r\n", "1\t363057\t363059\t0.000000\r\n", "1\t363078\t363080\t0.000000\r\n", "1\t363110\t363112\t0.000000\r\n", "1\t435752\t435754\t0.000000\r\n", "1\t525493\t525495\t0.000000\r\n", "1\t525498\t525500\t0.000000\r\n", "1\t525538\t525540\t0.000000\r\n", "1\t525578\t525580\t0.000000\r\n", "1\t525620\t525622\t0.000000\r\n", "\r\n", "==> Meth18_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-mcCDS <==\r\n", "1\t1733518\t1733520\t100.000000\r\n", "1\t1909757\t1909759\t60.000000\r\n", "1\t3129760\t3129762\t87.500000\r\n", "1\t3129772\t3129774\t100.000000\r\n", "1\t3129793\t3129795\t100.000000\r\n", "1\t3129805\t3129807\t100.000000\r\n", "2\t118829\t118831\t62.500000\r\n", "2\t118909\t118911\t80.000000\r\n", "2\t118926\t118928\t100.000000\r\n", "2\t118935\t118937\t100.000000\r\n", "\r\n", "==> Meth18_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-mcCDS <==\r\n", "1\t480696\t480698\t20.000000\r\n", "1\t667790\t667792\t40.000000\r\n", "1\t1045868\t1045870\t20.000000\r\n", "1\t1045903\t1045905\t20.000000\r\n", "1\t1046004\t1046006\t20.000000\r\n", "1\t1174923\t1174925\t40.000000\r\n", "1\t2303552\t2303554\t16.666667\r\n", "1\t2974502\t2974504\t40.000000\r\n", "1\t3197138\t3197140\t20.000000\r\n", "2\t118754\t118756\t42.857143\r\n", "\r\n", "==> Meth18_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-mcCDS <==\r\n", "1\t354586\t354588\t0.000000\r\n", "1\t401787\t401789\t0.000000\r\n", "1\t435464\t435466\t0.000000\r\n", "1\t480736\t480738\t0.000000\r\n", "1\t601787\t601789\t0.000000\r\n", "1\t601793\t601795\t0.000000\r\n", "1\t667800\t667802\t0.000000\r\n", "1\t780330\t780332\t0.000000\r\n", "1\t780338\t780340\t0.000000\r\n", "1\t780352\t780354\t0.000000\r\n", "\r\n", "==> Meth18_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-mcCDS <==\r\n", "1\t354586\t354588\t0.000000\r\n", "1\t401787\t401789\t0.000000\r\n", "1\t435464\t435466\t0.000000\r\n", "1\t480696\t480698\t20.000000\r\n", "1\t480736\t480738\t0.000000\r\n", "1\t601787\t601789\t0.000000\r\n", "1\t601793\t601795\t0.000000\r\n", "1\t667790\t667792\t40.000000\r\n", "1\t667800\t667802\t0.000000\r\n", "1\t780330\t780332\t0.000000\r\n" ] } ], "source": [ "#Check output\n", "!head *mcCDS" ] }, { "cell_type": "code", "execution_count": 121, "metadata": { "collapsed": false, "scrolled": true }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ " 65130 Meth10_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-mcCDS\n", " 73299 Meth10_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-mcCDS\n", " 436741 Meth10_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-mcCDS\n", " 575170 Meth10_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-mcCDS\n", " 77455 Meth11_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-mcCDS\n", " 71044 Meth11_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-mcCDS\n", " 452286 Meth11_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-mcCDS\n", " 600785 Meth11_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-mcCDS\n", " 136303 Meth12_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-mcCDS\n", " 109527 Meth12_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-mcCDS\n", " 715372 Meth12_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-mcCDS\n", " 961202 Meth12_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-mcCDS\n", " 22125 Meth13_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-mcCDS\n", " 13774 Meth13_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-mcCDS\n", " 209674 Meth13_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-mcCDS\n", " 245573 Meth13_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-mcCDS\n", " 15512 Meth14_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-mcCDS\n", " 12773 Meth14_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-mcCDS\n", " 182068 Meth14_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-mcCDS\n", " 210353 Meth14_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-mcCDS\n", " 18408 Meth15_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-mcCDS\n", " 16764 Meth15_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-mcCDS\n", " 212331 Meth15_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-mcCDS\n", " 247503 Meth15_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-mcCDS\n", " 16367 Meth16_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-mcCDS\n", " 11719 Meth16_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-mcCDS\n", " 59549 Meth16_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-mcCDS\n", " 87635 Meth16_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-mcCDS\n", " 6740 Meth17_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-mcCDS\n", " 4419 Meth17_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-mcCDS\n", " 23941 Meth17_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-mcCDS\n", " 35100 Meth17_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-mcCDS\n", " 4560 Meth18_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-mcCDS\n", " 2294 Meth18_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-mcCDS\n", " 14421 Meth18_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-mcCDS\n", " 21275 Meth18_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-mcCDS\n", " 5969192 total\n" ] } ], "source": [ "#Count number of overlaps\n", "!wc -l *mcCDS" ] }, { "cell_type": "code", "execution_count": 122, "metadata": { "collapsed": true }, "outputs": [], "source": [ "!wc -l *mcCDS > Mcap-5x-mcCDS-counts.txt" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "#### 4d. Introns" ] }, { "cell_type": "code", "execution_count": 123, "metadata": { "collapsed": false, "scrolled": true }, "outputs": [], "source": [ "%%bash\n", "\n", "for f in *bed\n", "do\n", " /usr/local/bin/intersectBed \\\n", " -u \\\n", " -a ${f} \\\n", " -b ../../../genome-feature-files/Mcap.GFFannotation.intron.gff \\\n", " > ${f}-mcIntrons\n", "done" ] }, { "cell_type": "code", "execution_count": 124, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "==> Meth10_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-mcIntrons <==\r\n", "1\t103334\t103336\t100.000000\r\n", "1\t103347\t103349\t100.000000\r\n", "1\t103356\t103358\t100.000000\r\n", "1\t103360\t103362\t100.000000\r\n", "1\t103398\t103400\t100.000000\r\n", "1\t105953\t105955\t80.000000\r\n", "1\t106012\t106014\t50.000000\r\n", "1\t106155\t106157\t60.000000\r\n", "1\t106173\t106175\t66.666667\r\n", "1\t106216\t106218\t60.000000\r\n", "\r\n", "==> Meth10_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-mcIntrons <==\r\n", "1\t80133\t80135\t20.000000\r\n", "1\t106202\t106204\t40.000000\r\n", "1\t184227\t184229\t16.666667\r\n", "1\t323373\t323375\t14.285714\r\n", "1\t324004\t324006\t12.500000\r\n", "1\t324495\t324497\t16.666667\r\n", "1\t324782\t324784\t12.500000\r\n", "1\t327501\t327503\t14.285714\r\n", "1\t327818\t327820\t14.285714\r\n", "1\t331324\t331326\t20.000000\r\n", "\r\n", "==> Meth10_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-mcIntrons <==\r\n", "1\t42893\t42895\t0.000000\r\n", "1\t42959\t42961\t0.000000\r\n", "1\t42970\t42972\t0.000000\r\n", "1\t42977\t42979\t0.000000\r\n", "1\t43005\t43007\t0.000000\r\n", "1\t80015\t80017\t0.000000\r\n", "1\t80040\t80042\t0.000000\r\n", "1\t80077\t80079\t0.000000\r\n", "1\t80101\t80103\t0.000000\r\n", "1\t80107\t80109\t0.000000\r\n", "\r", "\r\n", "==> Meth10_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-mcIntrons <==\r\n", "1\t42893\t42895\t0.000000\r\n", "1\t42959\t42961\t0.000000\r\n", "1\t42970\t42972\t0.000000\r\n", "1\t42977\t42979\t0.000000\r\n", "1\t43005\t43007\t0.000000\r\n", "1\t80015\t80017\t0.000000\r\n", "1\t80040\t80042\t0.000000\r\n", "1\t80077\t80079\t0.000000\r\n", "1\t80101\t80103\t0.000000\r\n", "1\t80107\t80109\t0.000000\r\n", "\r\n", "==> Meth11_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-mcIntrons <==\r\n", "1\t69235\t69237\t100.000000\r\n", "1\t69271\t69273\t80.000000\r\n", "1\t69275\t69277\t100.000000\r\n", "1\t69451\t69453\t100.000000\r\n", "1\t69580\t69582\t100.000000\r\n", "1\t69584\t69586\t100.000000\r\n", "1\t69845\t69847\t100.000000\r\n", "1\t69983\t69985\t100.000000\r\n", "1\t70019\t70021\t100.000000\r\n", "1\t70068\t70070\t100.000000\r\n", "\r\n", "==> Meth11_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-mcIntrons <==\r\n", "1\t74928\t74930\t14.285714\r\n", "1\t324573\t324575\t16.666667\r\n", "1\t325051\t325053\t16.666667\r\n", "1\t325110\t325112\t20.000000\r\n", "1\t331130\t331132\t11.111111\r\n", "1\t334055\t334057\t20.000000\r\n", "1\t334782\t334784\t28.571429\r\n", "1\t334792\t334794\t16.666667\r\n", "1\t334973\t334975\t40.000000\r\n", "1\t334977\t334979\t40.000000\r\n", "\r\n", "==> Meth11_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-mcIntrons <==\r\n", "1\t75182\t75184\t0.000000\r\n", "1\t75306\t75308\t0.000000\r\n", "1\t77745\t77747\t0.000000\r\n", "1\t77838\t77840\t0.000000\r\n", "1\t77846\t77848\t0.000000\r\n", "1\t77876\t77878\t0.000000\r\n", "1\t77894\t77896\t0.000000\r\n", "1\t78111\t78113\t0.000000\r\n", "1\t78135\t78137\t0.000000\r\n", "1\t78140\t78142\t0.000000\r\n", "\r\n", "==> Meth11_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-mcIntrons <==\r\n", "1\t69235\t69237\t100.000000\r\n", "1\t69271\t69273\t80.000000\r\n", "1\t69275\t69277\t100.000000\r\n", "1\t69451\t69453\t100.000000\r\n", "1\t69580\t69582\t100.000000\r\n", "1\t69584\t69586\t100.000000\r\n", "1\t69845\t69847\t100.000000\r\n", "1\t69983\t69985\t100.000000\r\n", "1\t70019\t70021\t100.000000\r\n", "1\t70068\t70070\t100.000000\r\n", "\r\n", "==> Meth12_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-mcIntrons <==\r\n", "1\t65972\t65974\t100.000000\r\n", "1\t65978\t65980\t100.000000\r\n", "1\t66345\t66347\t100.000000\r\n", "1\t66354\t66356\t100.000000\r\n", "1\t66980\t66982\t80.000000\r\n", "1\t67551\t67553\t80.000000\r\n", "1\t67834\t67836\t100.000000\r\n", "1\t67890\t67892\t100.000000\r\n", "1\t68059\t68061\t100.000000\r\n", "1\t68394\t68396\t80.000000\r\n", "\r\n", "==> Meth12_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-mcIntrons <==\r\n", "1\t23202\t23204\t12.500000\r\n", "1\t23382\t23384\t33.333333\r\n", "1\t23425\t23427\t20.000000\r\n", "1\t42323\t42325\t20.000000\r\n", "1\t45844\t45846\t28.571429\r\n", "1\t45913\t45915\t12.500000\r\n", "1\t45949\t45951\t12.500000\r\n", "1\t46485\t46487\t12.500000\r\n", "1\t48831\t48833\t20.000000\r\n", "1\t48881\t48883\t20.000000\r\n", "\r\n", "==> Meth12_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-mcIntrons <==\r\n", "1\t23003\t23005\t0.000000\r\n", "1\t23006\t23008\t0.000000\r\n", "1\t23019\t23021\t0.000000\r\n", "1\t23139\t23141\t0.000000\r\n", "1\t23173\t23175\t0.000000\r\n", "1\t23326\t23328\t0.000000\r\n", "1\t23334\t23336\t0.000000\r\n", "1\t23404\t23406\t0.000000\r\n", "1\t23445\t23447\t0.000000\r\n", "1\t38217\t38219\t0.000000\r\n", "\r\n", "==> Meth12_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-mcIntrons <==\r\n", "1\t23003\t23005\t0.000000\r\n", "1\t23006\t23008\t0.000000\r\n", "1\t23019\t23021\t0.000000\r\n", "1\t23139\t23141\t0.000000\r\n", "1\t23173\t23175\t0.000000\r\n", "1\t23202\t23204\t12.500000\r\n", "1\t23326\t23328\t0.000000\r\n", "1\t23334\t23336\t0.000000\r\n", "1\t23382\t23384\t33.333333\r\n", "1\t23404\t23406\t0.000000\r\n", "\r\n", "==> Meth13_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-mcIntrons <==\r\n", "1\t66041\t66043\t100.000000\r\n", "1\t66050\t66052\t100.000000\r\n", "1\t66339\t66341\t88.888889\r\n", "1\t66345\t66347\t77.777778\r\n", "1\t66354\t66356\t77.777778\r\n", "1\t66400\t66402\t100.000000\r\n", "1\t66540\t66542\t100.000000\r\n", "1\t66543\t66545\t100.000000\r\n", "1\t66613\t66615\t100.000000\r\n", "1\t66668\t66670\t100.000000\r\n", "\r\n", "==> Meth13_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-mcIntrons <==\r\n", "1\t48370\t48372\t14.285714\r\n", "1\t89011\t89013\t14.285714\r\n", "1\t332927\t332929\t25.000000\r\n", "1\t336069\t336071\t28.342246\r\n", "1\t336217\t336219\t33.673469\r\n", "1\t349633\t349635\t13.978495\r\n", "1\t369283\t369285\t10.638298\r\n", "1\t369679\t369681\t11.688312\r\n", "1\t372648\t372650\t18.750000\r\n", "1\t533612\t533614\t13.924051\r\n", "\r\n", "==> Meth13_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-mcIntrons <==\r\n", "1\t23117\t23119\t0.000000\r\n", "1\t23139\t23141\t0.000000\r\n", "1\t23173\t23175\t2.222222\r\n", "1\t23202\t23204\t0.000000\r\n", "1\t23326\t23328\t2.222222\r\n", "1\t23334\t23336\t1.123596\r\n", "1\t23382\t23384\t8.333333\r\n", "1\t39433\t39435\t0.000000\r\n", "1\t39477\t39479\t0.000000\r\n", "1\t39509\t39511\t0.000000\r\n", "\r\n", "==> Meth13_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-mcIntrons <==\r\n", "1\t23117\t23119\t0.000000\r\n", "1\t23139\t23141\t0.000000\r\n", "1\t23173\t23175\t2.222222\r\n", "1\t23202\t23204\t0.000000\r\n", "1\t23326\t23328\t2.222222\r\n", "1\t23334\t23336\t1.123596\r\n", "1\t23382\t23384\t8.333333\r\n", "1\t39433\t39435\t0.000000\r\n", "1\t39477\t39479\t0.000000\r\n", "1\t39509\t39511\t0.000000\r\n", "\r\n", "==> Meth14_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-mcIntrons <==\r\n", "1\t105822\t105824\t100.000000\r\n", "1\t105825\t105827\t100.000000\r\n", "1\t105836\t105838\t100.000000\r\n", "1\t105874\t105876\t100.000000\r\n", "1\t105883\t105885\t87.500000\r\n", "1\t105953\t105955\t50.000000\r\n", "1\t106012\t106014\t87.500000\r\n", "1\t106039\t106041\t100.000000\r\n", "1\t106049\t106051\t100.000000\r\n", "1\t106086\t106088\t100.000000\r\n", "\r\n", "==> Meth14_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-mcIntrons <==\r\n", "1\t124833\t124835\t20.000000\r\n", "1\t135853\t135855\t33.333333\r\n", "1\t323888\t323890\t10.526316\r\n", "1\t336069\t336071\t13.385827\r\n", "1\t344217\t344219\t11.846690\r\n", "1\t349633\t349635\t11.764706\r\n", "1\t367234\t367236\t11.486486\r\n", "1\t484816\t484818\t13.709677\r\n", "1\t527706\t527708\t23.469388\r\n", "1\t527726\t527728\t14.659686\r\n", "\r\n", "==> Meth14_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-mcIntrons <==\r\n", "1\t40450\t40452\t0.000000\r\n", "1\t40486\t40488\t0.000000\r\n", "1\t40541\t40543\t0.000000\r\n", "1\t40552\t40554\t0.000000\r\n", "1\t40555\t40557\t0.000000\r\n", "1\t42285\t42287\t0.000000\r\n", "1\t42304\t42306\t0.000000\r\n", "1\t42313\t42315\t0.000000\r\n", "1\t42323\t42325\t0.000000\r\n", "1\t42327\t42329\t0.000000\r\n", "\r\n", "==> Meth14_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-mcIntrons <==\r\n", "1\t40450\t40452\t0.000000\r\n", "1\t40486\t40488\t0.000000\r\n", "1\t40541\t40543\t0.000000\r\n", "1\t40552\t40554\t0.000000\r\n", "1\t40555\t40557\t0.000000\r\n", "1\t42285\t42287\t0.000000\r\n", "1\t42304\t42306\t0.000000\r\n", "1\t42313\t42315\t0.000000\r\n", "1\t42323\t42325\t0.000000\r\n", "1\t42327\t42329\t0.000000\r\n", "\r\n", "==> Meth15_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-mcIntrons <==\r\n", "1\t101462\t101464\t90.476190\r\n", "1\t101535\t101537\t100.000000\r\n", "1\t108751\t108753\t100.000000\r\n", "1\t108778\t108780\t100.000000\r\n", "1\t108787\t108789\t82.758621\r\n", "1\t108803\t108805\t100.000000\r\n", "1\t108815\t108817\t86.206897\r\n", "1\t108867\t108869\t100.000000\r\n", "1\t108949\t108951\t84.615385\r\n", "1\t344358\t344360\t100.000000\r\n", "\r\n", "==> Meth15_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-mcIntrons <==\r\n", "1\t41916\t41918\t13.043478\r\n", "1\t42261\t42263\t16.666667\r\n", "1\t78269\t78271\t22.222222\r\n", "1\t101503\t101505\t31.428571\r\n", "1\t101545\t101547\t40.000000\r\n", "1\t332804\t332806\t11.764706\r\n", "1\t336069\t336071\t20.496894\r\n", "1\t336217\t336219\t36.666667\r\n", "1\t339303\t339305\t20.000000\r\n", "1\t370881\t370883\t16.129032\r\n", "\r\n", "==> Meth15_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-mcIntrons <==\r\n", "1\t40450\t40452\t2.816901\r\n", "1\t40486\t40488\t0.000000\r\n", "1\t40541\t40543\t0.826446\r\n", "1\t40552\t40554\t0.000000\r\n", "1\t40555\t40557\t9.803922\r\n", "1\t41832\t41834\t0.000000\r\n", "1\t41845\t41847\t0.000000\r\n", "1\t41864\t41866\t0.000000\r\n", "1\t41974\t41976\t0.000000\r\n", "1\t42117\t42119\t4.347826\r\n", "\r\n", "==> Meth15_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-mcIntrons <==\r\n", "1\t40450\t40452\t2.816901\r\n", "1\t40486\t40488\t0.000000\r\n", "1\t40541\t40543\t0.826446\r\n", "1\t40552\t40554\t0.000000\r\n", "1\t40555\t40557\t9.803922\r\n", "1\t41832\t41834\t0.000000\r\n", "1\t41845\t41847\t0.000000\r\n", "1\t41864\t41866\t0.000000\r\n", "1\t41916\t41918\t13.043478\r\n", "1\t41974\t41976\t0.000000\r\n", "\r\n", "==> Meth16_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-mcIntrons <==\r\n", "1\t344031\t344033\t50.000000\r\n", "1\t344044\t344046\t60.000000\r\n", "1\t879915\t879917\t100.000000\r\n", "1\t883893\t883895\t50.000000\r\n", "1\t982886\t982888\t60.000000\r\n", "1\t1259506\t1259508\t100.000000\r\n", "1\t1259529\t1259531\t100.000000\r\n", "1\t1259533\t1259535\t100.000000\r\n", "1\t1259535\t1259537\t83.333333\r\n", "1\t1259538\t1259540\t83.333333\r\n", "\r\n", "==> Meth16_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-mcIntrons <==\r\n", "1\t328382\t328384\t20.000000\r\n", "1\t328386\t328388\t20.000000\r\n", "1\t330194\t330196\t20.000000\r\n", "1\t330197\t330199\t20.000000\r\n", "1\t334750\t334752\t14.285714\r\n", "1\t334782\t334784\t14.285714\r\n", "1\t341742\t341744\t20.000000\r\n", "1\t343939\t343941\t28.571429\r\n", "1\t343962\t343964\t42.857143\r\n", "1\t344000\t344002\t28.571429\r\n", "\r\n", "==> Meth16_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-mcIntrons <==\r\n", "1\t77096\t77098\t0.000000\r\n", "1\t77145\t77147\t0.000000\r\n", "1\t77151\t77153\t0.000000\r\n", "1\t77179\t77181\t0.000000\r\n", "1\t81812\t81814\t0.000000\r\n", "1\t81817\t81819\t0.000000\r\n", "1\t81835\t81837\t0.000000\r\n", "1\t81874\t81876\t0.000000\r\n", "1\t81887\t81889\t0.000000\r\n", "1\t323150\t323152\t0.000000\r\n", "\r\n", "==> Meth16_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-mcIntrons <==\r\n", "1\t77096\t77098\t0.000000\r\n", "1\t77145\t77147\t0.000000\r\n", "1\t77151\t77153\t0.000000\r\n", "1\t77179\t77181\t0.000000\r\n", "1\t81812\t81814\t0.000000\r\n", "1\t81817\t81819\t0.000000\r\n", "1\t81835\t81837\t0.000000\r\n", "1\t81874\t81876\t0.000000\r\n", "1\t81887\t81889\t0.000000\r\n", "1\t323150\t323152\t0.000000\r\n", "\r\n", "==> Meth17_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-mcIntrons <==\r\n", "1\t106173\t106175\t100.000000\r\n", "1\t106202\t106204\t100.000000\r\n", "1\t1243019\t1243021\t60.000000\r\n", "1\t1419093\t1419095\t87.500000\r\n", "1\t1457412\t1457414\t100.000000\r\n", "1\t1457444\t1457446\t80.000000\r\n", "1\t1457447\t1457449\t100.000000\r\n", "1\t1457450\t1457452\t100.000000\r\n", "1\t1457470\t1457472\t80.000000\r\n", "1\t1457490\t1457492\t100.000000\r\n", "\r\n", "==> Meth17_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-mcIntrons <==\r\n", "1\t884009\t884011\t20.000000\r\n", "1\t890256\t890258\t28.571429\r\n", "1\t890269\t890271\t14.285714\r\n", "1\t1123450\t1123452\t20.000000\r\n", "1\t1125135\t1125137\t20.000000\r\n", "1\t1128915\t1128917\t14.285714\r\n", "1\t1174476\t1174478\t40.000000\r\n", "1\t1248032\t1248034\t20.000000\r\n", "1\t1457456\t1457458\t40.000000\r\n", "1\t1572320\t1572322\t20.000000\r\n", "\r\n", "==> Meth17_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-mcIntrons <==\r\n", "1\t324616\t324618\t0.000000\r\n", "1\t336227\t336229\t0.000000\r\n", "1\t336251\t336253\t0.000000\r\n", "1\t336289\t336291\t0.000000\r\n", "1\t336307\t336309\t0.000000\r\n", "1\t336371\t336373\t0.000000\r\n", "1\t336396\t336398\t0.000000\r\n", "1\t336403\t336405\t0.000000\r\n", "1\t336423\t336425\t0.000000\r\n", "1\t336427\t336429\t0.000000\r\n", "\r\n", "==> Meth17_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-mcIntrons <==\r\n", "1\t106173\t106175\t100.000000\r\n", "1\t106202\t106204\t100.000000\r\n", "1\t324616\t324618\t0.000000\r\n", "1\t336227\t336229\t0.000000\r\n", "1\t336251\t336253\t0.000000\r\n", "1\t336289\t336291\t0.000000\r\n", "1\t336307\t336309\t0.000000\r\n", "1\t336371\t336373\t0.000000\r\n", "1\t336396\t336398\t0.000000\r\n", "1\t336403\t336405\t0.000000\r\n", "\r\n", "==> Meth18_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-mcIntrons <==\r\n", "1\t1468323\t1468325\t100.000000\r\n", "1\t1468670\t1468672\t100.000000\r\n", "1\t1468680\t1468682\t100.000000\r\n", "1\t1468683\t1468685\t100.000000\r\n", "1\t1468693\t1468695\t100.000000\r\n", "1\t1468700\t1468702\t100.000000\r\n", "1\t1468710\t1468712\t100.000000\r\n", "1\t1468737\t1468739\t100.000000\r\n", "1\t1468744\t1468746\t100.000000\r\n", "1\t1468749\t1468751\t100.000000\r\n", "\r\n", "==> Meth18_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-mcIntrons <==\r\n", "1\t889205\t889207\t20.000000\r\n", "1\t906918\t906920\t20.000000\r\n", "1\t906936\t906938\t16.666667\r\n", "1\t1131883\t1131885\t20.000000\r\n", "1\t1131892\t1131894\t20.000000\r\n", "1\t1131912\t1131914\t20.000000\r\n", "1\t1489883\t1489885\t20.000000\r\n", "1\t1768490\t1768492\t25.000000\r\n", "1\t1768499\t1768501\t25.000000\r\n", "1\t1768501\t1768503\t37.500000\r\n", "\r\n", "==> Meth18_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-mcIntrons <==\r\n", "1\t324315\t324317\t0.000000\r\n", "1\t324332\t324334\t0.000000\r\n", "1\t324348\t324350\t0.000000\r\n", "1\t324368\t324370\t0.000000\r\n", "1\t324424\t324426\t0.000000\r\n", "1\t374059\t374061\t0.000000\r\n", "1\t374080\t374082\t0.000000\r\n", "1\t435491\t435493\t0.000000\r\n", "1\t435513\t435515\t0.000000\r\n", "1\t440910\t440912\t0.000000\r\n", "\r\n", "==> Meth18_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-mcIntrons <==\r\n", "1\t324315\t324317\t0.000000\r\n", "1\t324332\t324334\t0.000000\r\n", "1\t324348\t324350\t0.000000\r\n", "1\t324368\t324370\t0.000000\r\n", "1\t324424\t324426\t0.000000\r\n", "1\t374059\t374061\t0.000000\r\n", "1\t374080\t374082\t0.000000\r\n", "1\t435491\t435493\t0.000000\r\n", "1\t435513\t435515\t0.000000\r\n", "1\t440910\t440912\t0.000000\r\n" ] } ], "source": [ "#Check output\n", "!head *mcIntrons" ] }, { "cell_type": "code", "execution_count": 125, "metadata": { "collapsed": false, "scrolled": true }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ " 234676 Meth10_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-mcIntrons\n", " 183802 Meth10_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-mcIntrons\n", " 1187161 Meth10_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-mcIntrons\n", " 1605639 Meth10_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-mcIntrons\n", " 271029 Meth11_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-mcIntrons\n", " 176456 Meth11_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-mcIntrons\n", " 1206084 Meth11_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-mcIntrons\n", " 1653569 Meth11_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-mcIntrons\n", " 554521 Meth12_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-mcIntrons\n", " 348649 Meth12_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-mcIntrons\n", " 2308024 Meth12_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-mcIntrons\n", " 3211194 Meth12_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-mcIntrons\n", " 136598 Meth13_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-mcIntrons\n", " 56017 Meth13_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-mcIntrons\n", " 948336 Meth13_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-mcIntrons\n", " 1140951 Meth13_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-mcIntrons\n", " 99217 Meth14_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-mcIntrons\n", " 50839 Meth14_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-mcIntrons\n", " 801092 Meth14_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-mcIntrons\n", " 951148 Meth14_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-mcIntrons\n", " 126464 Meth15_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-mcIntrons\n", " 66603 Meth15_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-mcIntrons\n", " 942556 Meth15_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-mcIntrons\n", " 1135623 Meth15_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-mcIntrons\n", " 47509 Meth16_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-mcIntrons\n", " 21593 Meth16_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-mcIntrons\n", " 115854 Meth16_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-mcIntrons\n", " 184956 Meth16_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-mcIntrons\n", " 20191 Meth17_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-mcIntrons\n", " 7902 Meth17_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-mcIntrons\n", " 45375 Meth17_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-mcIntrons\n", " 73468 Meth17_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-mcIntrons\n", " 12145 Meth18_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-mcIntrons\n", " 4187 Meth18_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-mcIntrons\n", " 28528 Meth18_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-mcIntrons\n", " 44860 Meth18_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-mcIntrons\n", " 20002816 total\n" ] } ], "source": [ "#Count number of overlaps\n", "!wc -l *mcIntrons" ] }, { "cell_type": "code", "execution_count": 126, "metadata": { "collapsed": true }, "outputs": [], "source": [ "!wc -l *mcIntrons > Mcap-5x-mcIntrons-counts.txt" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "#### 4e. Flanking regions" ] }, { "cell_type": "code", "execution_count": 127, "metadata": { "collapsed": false, "scrolled": true }, "outputs": [], "source": [ "%%bash\n", "\n", "for f in *bed\n", "do\n", " /usr/local/bin/intersectBed \\\n", " -u \\\n", " -a ${f} \\\n", " -b ../../../genome-feature-files/Mcap.GFFannotation.flanks.gff \\\n", " > ${f}-mcFlanks\n", "done" ] }, { "cell_type": "code", "execution_count": 128, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "==> Meth10_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-mcFlanks <==\r\n", "1\t443126\t443128\t60.000000\r\n", "1\t444404\t444406\t62.500000\r\n", "1\t1392759\t1392761\t50.000000\r\n", "1\t1392780\t1392782\t57.142857\r\n", "1\t1392793\t1392795\t57.142857\r\n", "1\t1392832\t1392834\t66.666667\r\n", "1\t1392838\t1392840\t60.000000\r\n", "1\t1392908\t1392910\t60.000000\r\n", "1\t1392921\t1392923\t60.000000\r\n", "1\t1396199\t1396201\t60.000000\r\n", "\r\n", "==> Meth10_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-mcFlanks <==\r\n", "1\t27782\t27784\t20.000000\r\n", "1\t148080\t148082\t16.666667\r\n", "1\t150099\t150101\t40.000000\r\n", "1\t182756\t182758\t20.000000\r\n", "1\t185808\t185810\t20.000000\r\n", "1\t185814\t185816\t20.000000\r\n", "1\t185830\t185832\t20.000000\r\n", "1\t185844\t185846\t16.666667\r\n", "1\t185868\t185870\t16.666667\r\n", "1\t185879\t185881\t14.285714\r\n", "\r\n", "==> Meth10_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-mcFlanks <==\r\n", "1\t27606\t27608\t0.000000\r\n", "1\t27613\t27615\t0.000000\r\n", "1\t27641\t27643\t0.000000\r\n", "1\t27643\t27645\t0.000000\r\n", "1\t27674\t27676\t0.000000\r\n", "1\t27718\t27720\t0.000000\r\n", "1\t27741\t27743\t0.000000\r\n", "1\t27758\t27760\t0.000000\r\n", "1\t27760\t27762\t0.000000\r\n", "1\t27768\t27770\t0.000000\r\n", "\r\n", "==> Meth10_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-mcFlanks <==\r\n", "1\t27606\t27608\t0.000000\r\n", "1\t27613\t27615\t0.000000\r\n", "1\t27641\t27643\t0.000000\r\n", "1\t27643\t27645\t0.000000\r\n", "1\t27674\t27676\t0.000000\r\n", "1\t27718\t27720\t0.000000\r\n", "1\t27741\t27743\t0.000000\r\n", "1\t27758\t27760\t0.000000\r\n", "1\t27760\t27762\t0.000000\r\n", "1\t27768\t27770\t0.000000\r\n", "\r\n", "==> Meth11_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-mcFlanks <==\r\n", "1\t443126\t443128\t71.428571\r\n", "1\t444404\t444406\t100.000000\r\n", "1\t788990\t788992\t60.000000\r\n", "1\t788995\t788997\t60.000000\r\n", "1\t1396199\t1396201\t55.555556\r\n", "1\t1426966\t1426968\t85.714286\r\n", "1\t1454029\t1454031\t88.888889\r\n", "1\t1454043\t1454045\t100.000000\r\n", "1\t1454631\t1454633\t100.000000\r\n", "1\t1454657\t1454659\t100.000000\r\n", "\r\n", "==> Meth11_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-mcFlanks <==\r\n", "1\t217374\t217376\t16.666667\r\n", "1\t217399\t217401\t14.285714\r\n", "1\t237189\t237191\t14.285714\r\n", "1\t307132\t307134\t20.000000\r\n", "1\t332179\t332181\t33.333333\r\n", "1\t332213\t332215\t20.000000\r\n", "1\t349077\t349079\t16.666667\r\n", "1\t357091\t357093\t14.285714\r\n", "1\t357122\t357124\t16.666667\r\n", "1\t357397\t357399\t22.222222\r\n", "\r\n", "==> Meth11_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-mcFlanks <==\r\n", "1\t217269\t217271\t0.000000\r\n", "1\t217349\t217351\t0.000000\r\n", "1\t217355\t217357\t0.000000\r\n", "1\t217384\t217386\t0.000000\r\n", "1\t218438\t218440\t0.000000\r\n", "1\t218447\t218449\t0.000000\r\n", "1\t218467\t218469\t0.000000\r\n", "1\t218477\t218479\t0.000000\r\n", "1\t218506\t218508\t0.000000\r\n", "1\t218532\t218534\t0.000000\r\n", "\r\n", "==> Meth11_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-mcFlanks <==\r\n", "1\t217269\t217271\t0.000000\r\n", "1\t217349\t217351\t0.000000\r\n", "1\t217355\t217357\t0.000000\r\n", "1\t217374\t217376\t16.666667\r\n", "1\t217384\t217386\t0.000000\r\n", "1\t217399\t217401\t14.285714\r\n", "1\t218438\t218440\t0.000000\r\n", "1\t218447\t218449\t0.000000\r\n", "1\t218467\t218469\t0.000000\r\n", "1\t218477\t218479\t0.000000\r\n", "\r\n", "==> Meth12_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-mcFlanks <==\r\n", "1\t443089\t443091\t50.000000\r\n", "1\t443126\t443128\t50.000000\r\n", "1\t789333\t789335\t70.000000\r\n", "1\t1063334\t1063336\t50.000000\r\n", "1\t1361040\t1361042\t100.000000\r\n", "1\t1361043\t1361045\t100.000000\r\n", "1\t1396199\t1396201\t80.000000\r\n", "1\t1425370\t1425372\t100.000000\r\n", "1\t1426944\t1426946\t100.000000\r\n", "1\t1426966\t1426968\t100.000000\r\n", "\r\n", "==> Meth12_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-mcFlanks <==\r\n", "1\t19619\t19621\t14.285714\r\n", "1\t21881\t21883\t16.666667\r\n", "1\t22117\t22119\t16.666667\r\n", "1\t37164\t37166\t16.666667\r\n", "1\t37234\t37236\t20.000000\r\n", "1\t52526\t52528\t20.000000\r\n", "1\t63142\t63144\t14.285714\r\n", "1\t63547\t63549\t20.000000\r\n", "1\t63579\t63581\t20.000000\r\n", "1\t109745\t109747\t11.111111\r\n", "\r\n", "==> Meth12_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-mcFlanks <==\r\n", "1\t17709\t17711\t0.000000\r\n", "1\t17723\t17725\t0.000000\r\n", "1\t19418\t19420\t0.000000\r\n", "1\t19487\t19489\t0.000000\r\n", "1\t19533\t19535\t0.000000\r\n", "1\t19541\t19543\t0.000000\r\n", "1\t19554\t19556\t0.000000\r\n", "1\t19573\t19575\t0.000000\r\n", "1\t19590\t19592\t0.000000\r\n", "1\t19614\t19616\t0.000000\r\n", "\r\n", "==> Meth12_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-mcFlanks <==\r\n", "1\t17709\t17711\t0.000000\r\n", "1\t17723\t17725\t0.000000\r\n", "1\t19418\t19420\t0.000000\r\n", "1\t19487\t19489\t0.000000\r\n", "1\t19533\t19535\t0.000000\r\n", "1\t19541\t19543\t0.000000\r\n", "1\t19554\t19556\t0.000000\r\n", "1\t19573\t19575\t0.000000\r\n", "1\t19590\t19592\t0.000000\r\n", "1\t19614\t19616\t0.000000\r\n", "\r\n", "==> Meth13_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-mcFlanks <==\r\n", "1\t147722\t147724\t94.444444\r\n", "1\t147732\t147734\t100.000000\r\n", "1\t147767\t147769\t100.000000\r\n", "1\t147785\t147787\t100.000000\r\n", "1\t147794\t147796\t100.000000\r\n", "1\t147806\t147808\t100.000000\r\n", "1\t788995\t788997\t80.000000\r\n", "1\t1097223\t1097225\t80.000000\r\n", "1\t1501390\t1501392\t94.642857\r\n", "1\t1501624\t1501626\t96.428571\r\n", "\r\n", "==> Meth13_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-mcFlanks <==\r\n", "1\t21739\t21741\t13.636364\r\n", "1\t87492\t87494\t33.333333\r\n", "1\t322944\t322946\t13.333333\r\n", "1\t459465\t459467\t10.493827\r\n", "1\t580358\t580360\t14.594595\r\n", "1\t602056\t602058\t10.810811\r\n", "1\t644776\t644778\t12.000000\r\n", "1\t644781\t644783\t28.571429\r\n", "1\t701623\t701625\t16.129032\r\n", "1\t726460\t726462\t33.333333\r\n", "\r\n", "==> Meth13_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-mcFlanks <==\r\n", "1\t21757\t21759\t0.000000\r\n", "1\t21830\t21832\t0.000000\r\n", "1\t21840\t21842\t0.000000\r\n", "1\t21881\t21883\t6.666667\r\n", "1\t21967\t21969\t0.000000\r\n", "1\t21980\t21982\t0.000000\r\n", "1\t22008\t22010\t0.000000\r\n", "1\t22089\t22091\t0.000000\r\n", "1\t22106\t22108\t4.444444\r\n", "1\t22111\t22113\t5.882353\r\n", "\r\n", "==> Meth13_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-mcFlanks <==\r\n", "1\t21739\t21741\t13.636364\r\n", "1\t21757\t21759\t0.000000\r\n", "1\t21830\t21832\t0.000000\r\n", "1\t21840\t21842\t0.000000\r\n", "1\t21881\t21883\t6.666667\r\n", "1\t21967\t21969\t0.000000\r\n", "1\t21980\t21982\t0.000000\r\n", "1\t22008\t22010\t0.000000\r\n", "1\t22089\t22091\t0.000000\r\n", "1\t22106\t22108\t4.444444\r\n", "\r\n", "==> Meth14_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-mcFlanks <==\r\n", "1\t644781\t644783\t62.500000\r\n", "1\t1726224\t1726226\t100.000000\r\n", "1\t1726417\t1726419\t93.589744\r\n", "1\t1726438\t1726440\t100.000000\r\n", "1\t1852547\t1852549\t63.157895\r\n", "1\t1852631\t1852633\t50.000000\r\n", "1\t1874454\t1874456\t90.740741\r\n", "1\t1882718\t1882720\t89.285714\r\n", "1\t1882722\t1882724\t92.857143\r\n", "1\t1882729\t1882731\t100.000000\r\n", "\r\n", "==> Meth14_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-mcFlanks <==\r\n", "1\t305489\t305491\t11.111111\r\n", "1\t357091\t357093\t12.500000\r\n", "1\t357382\t357384\t13.043478\r\n", "1\t582707\t582709\t10.344828\r\n", "1\t634819\t634821\t10.638298\r\n", "1\t644776\t644778\t11.764706\r\n", "1\t701549\t701551\t31.578947\r\n", "1\t704539\t704541\t25.000000\r\n", "1\t743459\t743461\t21.739130\r\n", "1\t790796\t790798\t14.285714\r\n", "\r\n", "==> Meth14_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-mcFlanks <==\r\n", "1\t63596\t63598\t0.000000\r\n", "1\t63697\t63699\t0.000000\r\n", "1\t63763\t63765\t0.000000\r\n", "1\t63800\t63802\t0.000000\r\n", "1\t305242\t305244\t8.000000\r\n", "1\t305317\t305319\t0.000000\r\n", "1\t305384\t305386\t0.000000\r\n", "1\t322012\t322014\t0.000000\r\n", "1\t322018\t322020\t0.378788\r\n", "1\t322027\t322029\t0.757576\r\n", "\r\n", "==> Meth14_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-mcFlanks <==\r\n", "1\t63596\t63598\t0.000000\r\n", "1\t63697\t63699\t0.000000\r\n", "1\t63763\t63765\t0.000000\r\n", "1\t63800\t63802\t0.000000\r\n", "1\t305242\t305244\t8.000000\r\n", "1\t305317\t305319\t0.000000\r\n", "1\t305384\t305386\t0.000000\r\n", "1\t305489\t305491\t11.111111\r\n", "1\t322012\t322014\t0.000000\r\n", "1\t322018\t322020\t0.378788\r\n", "\r\n", "==> Meth15_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-mcFlanks <==\r\n", "1\t1097223\t1097225\t93.333333\r\n", "1\t1726224\t1726226\t97.222222\r\n", "1\t1726417\t1726419\t93.846154\r\n", "1\t1726438\t1726440\t88.571429\r\n", "1\t1774138\t1774140\t100.000000\r\n", "1\t1774164\t1774166\t70.000000\r\n", "1\t1774296\t1774298\t93.548387\r\n", "1\t1868165\t1868167\t66.666667\r\n", "1\t1868179\t1868181\t60.000000\r\n", "1\t1868187\t1868189\t80.000000\r\n", "\r\n", "==> Meth15_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-mcFlanks <==\r\n", "1\t185844\t185846\t25.000000\r\n", "1\t186587\t186589\t25.000000\r\n", "1\t237921\t237923\t28.571429\r\n", "1\t237941\t237943\t28.571429\r\n", "1\t357419\t357421\t11.111111\r\n", "1\t357504\t357506\t37.500000\r\n", "1\t357548\t357550\t33.333333\r\n", "1\t464415\t464417\t18.181818\r\n", "1\t464461\t464463\t12.500000\r\n", "1\t464466\t464468\t12.500000\r\n", "\r\n", "==> Meth15_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-mcFlanks <==\r\n", "1\t63596\t63598\t0.000000\r\n", "1\t63697\t63699\t0.000000\r\n", "1\t63763\t63765\t0.000000\r\n", "1\t63800\t63802\t0.000000\r\n", "1\t63838\t63840\t0.000000\r\n", "1\t63869\t63871\t0.000000\r\n", "1\t87364\t87366\t0.000000\r\n", "1\t87399\t87401\t0.000000\r\n", "1\t87440\t87442\t0.000000\r\n", "1\t87443\t87445\t0.000000\r\n", "\r\n", "==> Meth15_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-mcFlanks <==\r\n", "1\t63596\t63598\t0.000000\r\n", "1\t63697\t63699\t0.000000\r\n", "1\t63763\t63765\t0.000000\r\n", "1\t63800\t63802\t0.000000\r\n", "1\t63838\t63840\t0.000000\r\n", "1\t63869\t63871\t0.000000\r\n", "1\t87364\t87366\t0.000000\r\n", "1\t87399\t87401\t0.000000\r\n", "1\t87440\t87442\t0.000000\r\n", "1\t87443\t87445\t0.000000\r\n", "\r\n", "==> Meth16_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-mcFlanks <==\r\n", "1\t789213\t789215\t60.000000\r\n", "1\t2070697\t2070699\t60.000000\r\n", "1\t2070732\t2070734\t80.000000\r\n", "2\t126187\t126189\t100.000000\r\n", "2\t126190\t126192\t80.000000\r\n", "2\t126197\t126199\t100.000000\r\n", "2\t126199\t126201\t100.000000\r\n", "2\t197311\t197313\t100.000000\r\n", "2\t197321\t197323\t100.000000\r\n", "2\t197327\t197329\t100.000000\r\n", "\r\n", "==> Meth16_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-mcFlanks <==\r\n", "1\t217198\t217200\t14.285714\r\n", "1\t376288\t376290\t20.000000\r\n", "1\t458648\t458650\t20.000000\r\n", "1\t618323\t618325\t20.000000\r\n", "1\t743459\t743461\t40.000000\r\n", "1\t789254\t789256\t16.666667\r\n", "1\t789277\t789279\t20.000000\r\n", "1\t1276837\t1276839\t42.857143\r\n", "1\t1276872\t1276874\t16.666667\r\n", "1\t1708805\t1708807\t20.000000\r\n", "\r\n", "==> Meth16_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-mcFlanks <==\r\n", "1\t217219\t217221\t0.000000\r\n", "1\t217248\t217250\t0.000000\r\n", "1\t217269\t217271\t0.000000\r\n", "1\t237189\t237191\t0.000000\r\n", "1\t322944\t322946\t0.000000\r\n", "1\t322963\t322965\t0.000000\r\n", "1\t376283\t376285\t0.000000\r\n", "1\t396370\t396372\t0.000000\r\n", "1\t396377\t396379\t0.000000\r\n", "1\t401633\t401635\t0.000000\r\n", "\r\n", "==> Meth16_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-mcFlanks <==\r\n", "1\t217198\t217200\t14.285714\r\n", "1\t217219\t217221\t0.000000\r\n", "1\t217248\t217250\t0.000000\r\n", "1\t217269\t217271\t0.000000\r\n", "1\t237189\t237191\t0.000000\r\n", "1\t322944\t322946\t0.000000\r\n", "1\t322963\t322965\t0.000000\r\n", "1\t376283\t376285\t0.000000\r\n", "1\t376288\t376290\t20.000000\r\n", "1\t396370\t396372\t0.000000\r\n", "\r\n", "==> Meth17_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-mcFlanks <==\r\n", "2\t404608\t404610\t100.000000\r\n", "2\t404614\t404616\t100.000000\r\n", "2\t404620\t404622\t100.000000\r\n", "2\t404632\t404634\t60.000000\r\n", "2\t404643\t404645\t100.000000\r\n", "2\t451404\t451406\t100.000000\r\n", "2\t451408\t451410\t80.000000\r\n", "2\t2031416\t2031418\t60.000000\r\n", "2\t2167886\t2167888\t66.666667\r\n", "2\t2167889\t2167891\t80.000000\r\n", "\r\n", "==> Meth17_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-mcFlanks <==\r\n", "1\t376177\t376179\t16.666667\r\n", "1\t618190\t618192\t16.666667\r\n", "1\t618205\t618207\t14.285714\r\n", "1\t778795\t778797\t40.000000\r\n", "1\t944356\t944358\t16.666667\r\n", "1\t2084166\t2084168\t14.285714\r\n", "1\t2655894\t2655896\t16.666667\r\n", "1\t2724041\t2724043\t16.666667\r\n", "2\t961832\t961834\t16.666667\r\n", "2\t1069847\t1069849\t16.666667\r\n", "\r\n", "==> Meth17_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-mcFlanks <==\r\n", "1\t375501\t375503\t0.000000\r\n", "1\t375506\t375508\t0.000000\r\n", "1\t376200\t376202\t0.000000\r\n", "1\t376220\t376222\t0.000000\r\n", "1\t376235\t376237\t0.000000\r\n", "1\t376261\t376263\t0.000000\r\n", "1\t376283\t376285\t0.000000\r\n", "1\t376288\t376290\t0.000000\r\n", "1\t376319\t376321\t0.000000\r\n", "1\t460016\t460018\t0.000000\r\n", "\r\n", "==> Meth17_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-mcFlanks <==\r\n", "1\t375501\t375503\t0.000000\r\n", "1\t375506\t375508\t0.000000\r\n", "1\t376177\t376179\t16.666667\r\n", "1\t376200\t376202\t0.000000\r\n", "1\t376220\t376222\t0.000000\r\n", "1\t376235\t376237\t0.000000\r\n", "1\t376261\t376263\t0.000000\r\n", "1\t376283\t376285\t0.000000\r\n", "1\t376288\t376290\t0.000000\r\n", "1\t376319\t376321\t0.000000\r\n", "\r\n", "==> Meth18_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-mcFlanks <==\r\n", "2\t173804\t173806\t100.000000\r\n", "2\t173810\t173812\t100.000000\r\n", "2\t260911\t260913\t60.000000\r\n", "2\t301621\t301623\t60.000000\r\n", "2\t330280\t330282\t80.000000\r\n", "2\t330291\t330293\t75.000000\r\n", "2\t330308\t330310\t100.000000\r\n", "2\t330327\t330329\t90.909091\r\n", "2\t330330\t330332\t100.000000\r\n", "2\t330347\t330349\t92.307692\r\n", "\r\n", "==> Meth18_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-mcFlanks <==\r\n", "1\t646162\t646164\t20.000000\r\n", "1\t726420\t726422\t20.000000\r\n", "1\t1700903\t1700905\t14.285714\r\n", "1\t1700905\t1700907\t14.285714\r\n", "1\t1852209\t1852211\t20.000000\r\n", "1\t1970185\t1970187\t20.000000\r\n", "1\t3164844\t3164846\t20.000000\r\n", "1\t3164864\t3164866\t20.000000\r\n", "2\t330679\t330681\t16.666667\r\n", "2\t2122592\t2122594\t20.000000\r\n", "\r\n", "==> Meth18_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-mcFlanks <==\r", "\r\n", "1\t401736\t401738\t0.000000\r\n", "1\t401738\t401740\t0.000000\r\n", "1\t401743\t401745\t0.000000\r\n", "1\t401767\t401769\t0.000000\r\n", "1\t401776\t401778\t0.000000\r\n", "1\t458933\t458935\t0.000000\r\n", "1\t458950\t458952\t0.000000\r\n", "1\t585916\t585918\t0.000000\r\n", "1\t602056\t602058\t0.000000\r\n", "1\t622374\t622376\t0.000000\r\n", "\r\n", "==> Meth18_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-mcFlanks <==\r\n", "1\t401736\t401738\t0.000000\r\n", "1\t401738\t401740\t0.000000\r\n", "1\t401743\t401745\t0.000000\r\n", "1\t401767\t401769\t0.000000\r\n", "1\t401776\t401778\t0.000000\r\n", "1\t458933\t458935\t0.000000\r\n", "1\t458950\t458952\t0.000000\r\n", "1\t585916\t585918\t0.000000\r\n", "1\t602056\t602058\t0.000000\r\n", "1\t622374\t622376\t0.000000\r\n" ] } ], "source": [ "#Check output\n", "!head *mcFlanks" ] }, { "cell_type": "code", "execution_count": 129, "metadata": { "collapsed": false, "scrolled": true }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ " 48103 Meth10_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-mcFlanks\n", " 67167 Meth10_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-mcFlanks\n", " 410065 Meth10_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-mcFlanks\n", " 525335 Meth10_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-mcFlanks\n", " 56509 Meth11_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-mcFlanks\n", " 63147 Meth11_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-mcFlanks\n", " 417550 Meth11_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-mcFlanks\n", " 537206 Meth11_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-mcFlanks\n", " 116459 Meth12_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-mcFlanks\n", " 120157 Meth12_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-mcFlanks\n", " 779025 Meth12_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-mcFlanks\n", " 1015641 Meth12_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-mcFlanks\n", " 29100 Meth13_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-mcFlanks\n", " 18358 Meth13_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-mcFlanks\n", " 315284 Meth13_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-mcFlanks\n", " 362742 Meth13_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-mcFlanks\n", " 20401 Meth14_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-mcFlanks\n", " 16579 Meth14_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-mcFlanks\n", " 268266 Meth14_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-mcFlanks\n", " 305246 Meth14_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-mcFlanks\n", " 24948 Meth15_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-mcFlanks\n", " 21741 Meth15_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-mcFlanks\n", " 315952 Meth15_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-mcFlanks\n", " 362641 Meth15_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-mcFlanks\n", " 12593 Meth16_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-mcFlanks\n", " 8823 Meth16_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-mcFlanks\n", " 44466 Meth16_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-mcFlanks\n", " 65882 Meth16_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-mcFlanks\n", " 5449 Meth17_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-mcFlanks\n", " 3278 Meth17_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-mcFlanks\n", " 17161 Meth17_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-mcFlanks\n", " 25888 Meth17_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-mcFlanks\n", " 3831 Meth18_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-mcFlanks\n", " 1806 Meth18_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-mcFlanks\n", " 10698 Meth18_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-mcFlanks\n", " 16335 Meth18_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-mcFlanks\n", " 6433832 total\n" ] } ], "source": [ "#Count number of overlaps\n", "!wc -l *mcFlanks" ] }, { "cell_type": "code", "execution_count": 130, "metadata": { "collapsed": true }, "outputs": [], "source": [ "!wc -l *mcFlanks > Mcap-5x-mcFlanks-counts.txt" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "#### 4f. Upstream flanking regions" ] }, { "cell_type": "code", "execution_count": 131, "metadata": { "collapsed": false, "scrolled": true }, "outputs": [], "source": [ "%%bash\n", "\n", "for f in *bed\n", "do\n", " /usr/local/bin/intersectBed \\\n", " -u \\\n", " -a ${f} \\\n", " -b ../../../genome-feature-files/Mcap.GFFannotation.flanks.Upstream.gff \\\n", " > ${f}-mcFlanksUpstream\n", "done" ] }, { "cell_type": "code", "execution_count": 132, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "==> Meth10_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-mcFlanksUpstream <==\r\n", "1\t443126\t443128\t60.000000\r\n", "1\t444404\t444406\t62.500000\r\n", "1\t1820781\t1820783\t87.500000\r\n", "1\t1820794\t1820796\t100.000000\r\n", "1\t1820815\t1820817\t100.000000\r\n", "1\t1852344\t1852346\t60.000000\r\n", "1\t2135619\t2135621\t80.000000\r\n", "1\t2135646\t2135648\t80.000000\r\n", "1\t2135651\t2135653\t80.000000\r\n", "1\t2135655\t2135657\t71.428571\r\n", "\r\n", "==> Meth10_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-mcFlanksUpstream <==\r\n", "1\t27782\t27784\t20.000000\r\n", "1\t148080\t148082\t16.666667\r\n", "1\t182756\t182758\t20.000000\r\n", "1\t185808\t185810\t20.000000\r\n", "1\t185814\t185816\t20.000000\r\n", "1\t185830\t185832\t20.000000\r\n", "1\t185844\t185846\t16.666667\r\n", "1\t185868\t185870\t16.666667\r\n", "1\t185879\t185881\t14.285714\r\n", "1\t307046\t307048\t12.500000\r\n", "\r\n", "==> Meth10_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-mcFlanksUpstream <==\r\n", "1\t27606\t27608\t0.000000\r\n", "1\t27613\t27615\t0.000000\r\n", "1\t27641\t27643\t0.000000\r\n", "1\t27643\t27645\t0.000000\r\n", "1\t27674\t27676\t0.000000\r\n", "1\t27718\t27720\t0.000000\r\n", "1\t27741\t27743\t0.000000\r\n", "1\t27758\t27760\t0.000000\r\n", "1\t27760\t27762\t0.000000\r\n", "1\t27768\t27770\t0.000000\r\n", "\r\n", "==> Meth10_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-mcFlanksUpstream <==\r\n", "1\t27606\t27608\t0.000000\r\n", "1\t27613\t27615\t0.000000\r\n", "1\t27641\t27643\t0.000000\r\n", "1\t27643\t27645\t0.000000\r\n", "1\t27674\t27676\t0.000000\r\n", "1\t27718\t27720\t0.000000\r\n", "1\t27741\t27743\t0.000000\r\n", "1\t27758\t27760\t0.000000\r\n", "1\t27760\t27762\t0.000000\r\n", "1\t27768\t27770\t0.000000\r\n", "\r\n", "==> Meth11_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-mcFlanksUpstream <==\r\n", "1\t443126\t443128\t71.428571\r\n", "1\t444404\t444406\t100.000000\r\n", "1\t1820965\t1820967\t60.000000\r\n", "1\t1823619\t1823621\t80.000000\r\n", "1\t1852270\t1852272\t80.000000\r\n", "1\t1852483\t1852485\t66.666667\r\n", "1\t2136058\t2136060\t100.000000\r\n", "1\t2136128\t2136130\t100.000000\r\n", "1\t2136170\t2136172\t100.000000\r\n", "1\t2136193\t2136195\t100.000000\r\n", "\r\n", "==> Meth11_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-mcFlanksUpstream <==\r\n", "1\t237189\t237191\t14.285714\r\n", "1\t307132\t307134\t20.000000\r\n", "1\t332179\t332181\t33.333333\r\n", "1\t332213\t332215\t20.000000\r\n", "1\t349077\t349079\t16.666667\r\n", "1\t375660\t375662\t16.666667\r\n", "1\t376102\t376104\t20.000000\r\n", "1\t396306\t396308\t20.000000\r\n", "1\t401442\t401444\t12.500000\r\n", "1\t401654\t401656\t14.285714\r\n", "\r\n", "==> Meth11_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-mcFlanksUpstream <==\r\n", "1\t218438\t218440\t0.000000\r\n", "1\t218447\t218449\t0.000000\r\n", "1\t218467\t218469\t0.000000\r\n", "1\t218477\t218479\t0.000000\r\n", "1\t218506\t218508\t0.000000\r\n", "1\t218532\t218534\t0.000000\r\n", "1\t218623\t218625\t0.000000\r\n", "1\t237136\t237138\t0.000000\r\n", "1\t237161\t237163\t0.000000\r\n", "1\t237223\t237225\t0.000000\r\n", "\r\n", "==> Meth11_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-mcFlanksUpstream <==\r\n", "1\t218438\t218440\t0.000000\r\n", "1\t218447\t218449\t0.000000\r\n", "1\t218467\t218469\t0.000000\r\n", "1\t218477\t218479\t0.000000\r\n", "1\t218506\t218508\t0.000000\r\n", "1\t218532\t218534\t0.000000\r\n", "1\t218623\t218625\t0.000000\r\n", "1\t237136\t237138\t0.000000\r\n", "1\t237161\t237163\t0.000000\r\n", "1\t237189\t237191\t14.285714\r\n", "\r\n", "==> Meth12_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-mcFlanksUpstream <==\r\n", "1\t443089\t443091\t50.000000\r\n", "1\t443126\t443128\t50.000000\r\n", "1\t1063334\t1063336\t50.000000\r\n", "1\t1663471\t1663473\t57.142857\r\n", "1\t1663475\t1663477\t71.428571\r\n", "1\t1663486\t1663488\t50.000000\r\n", "1\t1663520\t1663522\t66.666667\r\n", "1\t1820794\t1820796\t83.333333\r\n", "1\t1820815\t1820817\t100.000000\r\n", "1\t1821354\t1821356\t100.000000\r\n", "\r\n", "==> Meth12_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-mcFlanksUpstream <==\r\n", "1\t19619\t19621\t14.285714\r\n", "1\t37164\t37166\t16.666667\r\n", "1\t37234\t37236\t20.000000\r\n", "1\t63142\t63144\t14.285714\r\n", "1\t63547\t63549\t20.000000\r\n", "1\t63579\t63581\t20.000000\r\n", "1\t109745\t109747\t11.111111\r\n", "1\t236994\t236996\t20.000000\r\n", "1\t308797\t308799\t20.000000\r\n", "1\t331983\t331985\t16.666667\r\n", "\r\n", "==> Meth12_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-mcFlanksUpstream <==\r\n", "1\t19418\t19420\t0.000000\r\n", "1\t19487\t19489\t0.000000\r\n", "1\t19533\t19535\t0.000000\r\n", "1\t19541\t19543\t0.000000\r\n", "1\t19554\t19556\t0.000000\r\n", "1\t19573\t19575\t0.000000\r\n", "1\t19590\t19592\t0.000000\r\n", "1\t19614\t19616\t0.000000\r\n", "1\t19617\t19619\t0.000000\r\n", "1\t19625\t19627\t0.000000\r\n", "\r\n", "==> Meth12_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-mcFlanksUpstream <==\r\n", "1\t19418\t19420\t0.000000\r\n", "1\t19487\t19489\t0.000000\r\n", "1\t19533\t19535\t0.000000\r\n", "1\t19541\t19543\t0.000000\r\n", "1\t19554\t19556\t0.000000\r\n", "1\t19573\t19575\t0.000000\r\n", "1\t19590\t19592\t0.000000\r\n", "1\t19614\t19616\t0.000000\r\n", "1\t19617\t19619\t0.000000\r\n", "1\t19619\t19621\t14.285714\r\n", "\r\n", "==> Meth13_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-mcFlanksUpstream <==\r\n", "1\t147722\t147724\t94.444444\r\n", "1\t147732\t147734\t100.000000\r\n", "1\t147767\t147769\t100.000000\r\n", "1\t147785\t147787\t100.000000\r\n", "1\t147794\t147796\t100.000000\r\n", "1\t147806\t147808\t100.000000\r\n", "1\t1097223\t1097225\t80.000000\r\n", "1\t1868165\t1868167\t60.000000\r\n", "1\t2135507\t2135509\t100.000000\r\n", "1\t2135516\t2135518\t100.000000\r\n", "\r\n", "==> Meth13_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-mcFlanksUpstream <==\r\n", "1\t87492\t87494\t33.333333\r\n", "1\t459465\t459467\t10.493827\r\n", "1\t644776\t644778\t12.000000\r\n", "1\t644781\t644783\t28.571429\r\n", "1\t726460\t726462\t33.333333\r\n", "1\t1024653\t1024655\t19.402985\r\n", "1\t1097233\t1097235\t11.111111\r\n", "1\t1097311\t1097313\t14.285714\r\n", "1\t1852483\t1852485\t20.000000\r\n", "1\t1852504\t1852506\t19.178082\r\n", "\r\n", "==> Meth13_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-mcFlanksUpstream <==\r\n", "1\t62755\t62757\t2.500000\r\n", "1\t62841\t62843\t1.234568\r\n", "1\t63350\t63352\t1.754386\r\n", "1\t63357\t63359\t2.173913\r\n", "1\t63369\t63371\t0.724638\r\n", "1\t63388\t63390\t0.000000\r\n", "1\t63390\t63392\t0.724638\r\n", "1\t63431\t63433\t1.449275\r\n", "1\t63443\t63445\t2.919708\r\n", "1\t63485\t63487\t0.724638\r\n", "\r\n", "==> Meth13_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-mcFlanksUpstream <==\r\n", "1\t62755\t62757\t2.500000\r\n", "1\t62841\t62843\t1.234568\r\n", "1\t63350\t63352\t1.754386\r\n", "1\t63357\t63359\t2.173913\r\n", "1\t63369\t63371\t0.724638\r\n", "1\t63388\t63390\t0.000000\r\n", "1\t63390\t63392\t0.724638\r\n", "1\t63431\t63433\t1.449275\r\n", "1\t63443\t63445\t2.919708\r\n", "1\t63485\t63487\t0.724638\r\n", "\r\n", "==> Meth14_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-mcFlanksUpstream <==\r\n", "1\t644781\t644783\t62.500000\r\n", "1\t1852547\t1852549\t63.157895\r\n", "1\t1852631\t1852633\t50.000000\r\n", "1\t2135794\t2135796\t100.000000\r\n", "1\t2135804\t2135806\t81.250000\r\n", "1\t2135806\t2135808\t93.750000\r\n", "1\t2135816\t2135818\t93.750000\r\n", "1\t2135829\t2135831\t100.000000\r\n", "1\t2135850\t2135852\t100.000000\r\n", "1\t2135875\t2135877\t100.000000\r\n", "\r\n", "==> Meth14_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-mcFlanksUpstream <==\r\n", "1\t582707\t582709\t10.344828\r\n", "1\t644776\t644778\t11.764706\r\n", "1\t704539\t704541\t25.000000\r\n", "1\t790796\t790798\t14.285714\r\n", "1\t1175900\t1175902\t25.000000\r\n", "1\t1177163\t1177165\t21.428571\r\n", "1\t1184006\t1184008\t19.148936\r\n", "1\t1276904\t1276906\t20.000000\r\n", "1\t1428622\t1428624\t15.384615\r\n", "1\t1443376\t1443378\t11.475410\r\n", "\r\n", "==> Meth14_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-mcFlanksUpstream <==\r\n", "1\t63596\t63598\t0.000000\r\n", "1\t63697\t63699\t0.000000\r\n", "1\t63763\t63765\t0.000000\r\n", "1\t63800\t63802\t0.000000\r\n", "1\t331983\t331985\t7.894737\r\n", "1\t332001\t332003\t0.462963\r\n", "1\t332015\t332017\t0.925926\r\n", "1\t332024\t332026\t0.000000\r\n", "1\t332034\t332036\t1.388889\r\n", "1\t332039\t332041\t0.462963\r\n", "\r\n", "==> Meth14_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-mcFlanksUpstream <==\r\n", "1\t63596\t63598\t0.000000\r\n", "1\t63697\t63699\t0.000000\r\n", "1\t63763\t63765\t0.000000\r\n", "1\t63800\t63802\t0.000000\r\n", "1\t331983\t331985\t7.894737\r\n", "1\t332001\t332003\t0.462963\r\n", "1\t332015\t332017\t0.925926\r\n", "1\t332024\t332026\t0.000000\r\n", "1\t332034\t332036\t1.388889\r\n", "1\t332039\t332041\t0.462963\r\n", "\r\n", "==> Meth15_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-mcFlanksUpstream <==\r\n", "1\t1097223\t1097225\t93.333333\r\n", "1\t1868165\t1868167\t66.666667\r\n", "1\t1868179\t1868181\t60.000000\r\n", "1\t1868187\t1868189\t80.000000\r\n", "1\t1868189\t1868191\t80.000000\r\n", "1\t1952909\t1952911\t83.333333\r\n", "1\t2135501\t2135503\t100.000000\r\n", "1\t2135507\t2135509\t100.000000\r\n", "1\t2135516\t2135518\t100.000000\r\n", "1\t2135519\t2135521\t100.000000\r\n", "\r\n", "==> Meth15_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-mcFlanksUpstream <==\r\n", "1\t185844\t185846\t25.000000\r\n", "1\t237921\t237923\t28.571429\r\n", "1\t237941\t237943\t28.571429\r\n", "1\t464415\t464417\t18.181818\r\n", "1\t464461\t464463\t12.500000\r\n", "1\t464466\t464468\t12.500000\r\n", "1\t491828\t491830\t11.627907\r\n", "1\t644525\t644527\t40.000000\r\n", "1\t644531\t644533\t40.000000\r\n", "1\t644543\t644545\t40.000000\r\n", "\r\n", "==> Meth15_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-mcFlanksUpstream <==\r\n", "1\t63596\t63598\t0.000000\r\n", "1\t63697\t63699\t0.000000\r\n", "1\t63763\t63765\t0.000000\r\n", "1\t63800\t63802\t0.000000\r\n", "1\t63838\t63840\t0.000000\r\n", "1\t63869\t63871\t0.000000\r\n", "1\t87364\t87366\t0.000000\r\n", "1\t87399\t87401\t0.000000\r\n", "1\t87440\t87442\t0.000000\r\n", "1\t87443\t87445\t0.000000\r\n", "\r\n", "==> Meth15_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-mcFlanksUpstream <==\r\n", "1\t63596\t63598\t0.000000\r\n", "1\t63697\t63699\t0.000000\r\n", "1\t63763\t63765\t0.000000\r\n", "1\t63800\t63802\t0.000000\r\n", "1\t63838\t63840\t0.000000\r\n", "1\t63869\t63871\t0.000000\r\n", "1\t87364\t87366\t0.000000\r\n", "1\t87399\t87401\t0.000000\r\n", "1\t87440\t87442\t0.000000\r\n", "1\t87443\t87445\t0.000000\r\n", "\r\n", "==> Meth16_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-mcFlanksUpstream <==\r\n", "2\t126187\t126189\t100.000000\r\n", "2\t126190\t126192\t80.000000\r\n", "2\t126197\t126199\t100.000000\r\n", "2\t126199\t126201\t100.000000\r\n", "2\t330679\t330681\t80.000000\r\n", "2\t389824\t389826\t80.000000\r\n", "2\t445154\t445156\t100.000000\r\n", "2\t445170\t445172\t85.714286\r\n", "2\t445172\t445174\t100.000000\r\n", "2\t445199\t445201\t100.000000\r\n", "\r\n", "==> Meth16_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-mcFlanksUpstream <==\r\n", "1\t376288\t376290\t20.000000\r\n", "1\t618323\t618325\t20.000000\r\n", "1\t1276837\t1276839\t42.857143\r\n", "1\t1276872\t1276874\t16.666667\r\n", "1\t1852075\t1852077\t20.000000\r\n", "1\t1852209\t1852211\t40.000000\r\n", "1\t1852233\t1852235\t20.000000\r\n", "1\t1852286\t1852288\t40.000000\r\n", "1\t1852291\t1852293\t40.000000\r\n", "1\t1852309\t1852311\t40.000000\r\n", "\r\n", "==> Meth16_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-mcFlanksUpstream <==\r\n", "1\t237189\t237191\t0.000000\r\n", "1\t376283\t376285\t0.000000\r\n", "1\t396370\t396372\t0.000000\r\n", "1\t396377\t396379\t0.000000\r\n", "1\t401633\t401635\t0.000000\r\n", "1\t434589\t434591\t0.000000\r\n", "1\t434639\t434641\t0.000000\r\n", "1\t435026\t435028\t0.000000\r\n", "1\t459556\t459558\t0.000000\r\n", "1\t459593\t459595\t0.000000\r\n", "\r\n", "==> Meth16_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-mcFlanksUpstream <==\r\n", "1\t237189\t237191\t0.000000\r\n", "1\t376283\t376285\t0.000000\r\n", "1\t376288\t376290\t20.000000\r\n", "1\t396370\t396372\t0.000000\r\n", "1\t396377\t396379\t0.000000\r\n", "1\t401633\t401635\t0.000000\r\n", "1\t434589\t434591\t0.000000\r\n", "1\t434639\t434641\t0.000000\r\n", "1\t435026\t435028\t0.000000\r\n", "1\t459556\t459558\t0.000000\r\n", "\r\n", "==> Meth17_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-mcFlanksUpstream <==\r\n", "2\t404608\t404610\t100.000000\r\n", "2\t404614\t404616\t100.000000\r\n", "2\t404620\t404622\t100.000000\r\n", "2\t404632\t404634\t60.000000\r\n", "2\t404643\t404645\t100.000000\r\n", "2\t451404\t451406\t100.000000\r\n", "2\t451408\t451410\t80.000000\r\n", "2\t2031416\t2031418\t60.000000\r\n", "2\t2881246\t2881248\t75.000000\r\n", "2\t2881267\t2881269\t90.909091\r\n", "\r\n", "==> Meth17_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-mcFlanksUpstream <==\r\n", "1\t376177\t376179\t16.666667\r\n", "1\t618190\t618192\t16.666667\r\n", "1\t618205\t618207\t14.285714\r\n", "1\t944356\t944358\t16.666667\r\n", "1\t2084166\t2084168\t14.285714\r\n", "2\t3078944\t3078946\t40.000000\r\n", "2\t3308682\t3308684\t20.000000\r\n", "4\t2285463\t2285465\t20.000000\r\n", "4\t2763291\t2763293\t45.000000\r\n", "5\t218528\t218530\t40.000000\r\n", "\r\n", "==> Meth17_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-mcFlanksUpstream <==\r\n", "1\t375501\t375503\t0.000000\r\n", "1\t375506\t375508\t0.000000\r\n", "1\t376200\t376202\t0.000000\r\n", "1\t376220\t376222\t0.000000\r\n", "1\t376235\t376237\t0.000000\r\n", "1\t376261\t376263\t0.000000\r\n", "1\t376283\t376285\t0.000000\r\n", "1\t376288\t376290\t0.000000\r\n", "1\t376319\t376321\t0.000000\r\n", "1\t460016\t460018\t0.000000\r\n", "\r\n", "==> Meth17_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-mcFlanksUpstream <==\r\n", "1\t375501\t375503\t0.000000\r\n", "1\t375506\t375508\t0.000000\r\n", "1\t376177\t376179\t16.666667\r\n", "1\t376200\t376202\t0.000000\r", "\r\n", "1\t376220\t376222\t0.000000\r\n", "1\t376235\t376237\t0.000000\r\n", "1\t376261\t376263\t0.000000\r\n", "1\t376283\t376285\t0.000000\r\n", "1\t376288\t376290\t0.000000\r\n", "1\t376319\t376321\t0.000000\r\n", "\r\n", "==> Meth18_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-mcFlanksUpstream <==\r\n", "2\t173804\t173806\t100.000000\r\n", "2\t173810\t173812\t100.000000\r\n", "2\t420160\t420162\t80.000000\r\n", "2\t468588\t468590\t100.000000\r\n", "2\t485672\t485674\t100.000000\r\n", "2\t485686\t485688\t100.000000\r\n", "2\t485690\t485692\t100.000000\r\n", "2\t485708\t485710\t100.000000\r\n", "2\t1844074\t1844076\t100.000000\r\n", "2\t2031196\t2031198\t100.000000\r\n", "\r\n", "==> Meth18_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-mcFlanksUpstream <==\r\n", "1\t726420\t726422\t20.000000\r\n", "1\t1700903\t1700905\t14.285714\r\n", "1\t1700905\t1700907\t14.285714\r\n", "1\t1852209\t1852211\t20.000000\r\n", "1\t1970185\t1970187\t20.000000\r\n", "1\t3164844\t3164846\t20.000000\r\n", "1\t3164864\t3164866\t20.000000\r\n", "2\t330679\t330681\t16.666667\r\n", "2\t2122592\t2122594\t20.000000\r\n", "4\t2767000\t2767002\t20.000000\r\n", "\r\n", "==> Meth18_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-mcFlanksUpstream <==\r\n", "1\t401736\t401738\t0.000000\r\n", "1\t401738\t401740\t0.000000\r\n", "1\t401743\t401745\t0.000000\r\n", "1\t401767\t401769\t0.000000\r\n", "1\t401776\t401778\t0.000000\r\n", "1\t622374\t622376\t0.000000\r\n", "1\t622376\t622378\t0.000000\r\n", "1\t622398\t622400\t0.000000\r\n", "1\t622400\t622402\t0.000000\r\n", "1\t622442\t622444\t0.000000\r\n", "\r\n", "==> Meth18_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-mcFlanksUpstream <==\r\n", "1\t401736\t401738\t0.000000\r\n", "1\t401738\t401740\t0.000000\r\n", "1\t401743\t401745\t0.000000\r\n", "1\t401767\t401769\t0.000000\r\n", "1\t401776\t401778\t0.000000\r\n", "1\t622374\t622376\t0.000000\r\n", "1\t622376\t622378\t0.000000\r\n", "1\t622398\t622400\t0.000000\r\n", "1\t622400\t622402\t0.000000\r\n", "1\t622442\t622444\t0.000000\r\n" ] } ], "source": [ "#Check output\n", "!head *mcFlanksUpstream" ] }, { "cell_type": "code", "execution_count": 133, "metadata": { "collapsed": false, "scrolled": true }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ " 27089 Meth10_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-mcFlanksUpstream\n", " 38010 Meth10_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-mcFlanksUpstream\n", " 227994 Meth10_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-mcFlanksUpstream\n", " 293093 Meth10_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-mcFlanksUpstream\n", " 31986 Meth11_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-mcFlanksUpstream\n", " 35374 Meth11_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-mcFlanksUpstream\n", " 231007 Meth11_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-mcFlanksUpstream\n", " 298367 Meth11_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-mcFlanksUpstream\n", " 65420 Meth12_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-mcFlanksUpstream\n", " 66325 Meth12_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-mcFlanksUpstream\n", " 428131 Meth12_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-mcFlanksUpstream\n", " 559876 Meth12_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-mcFlanksUpstream\n", " 16752 Meth13_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-mcFlanksUpstream\n", " 10225 Meth13_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-mcFlanksUpstream\n", " 177270 Meth13_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-mcFlanksUpstream\n", " 204247 Meth13_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-mcFlanksUpstream\n", " 11869 Meth14_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-mcFlanksUpstream\n", " 9441 Meth14_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-mcFlanksUpstream\n", " 151453 Meth14_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-mcFlanksUpstream\n", " 172763 Meth14_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-mcFlanksUpstream\n", " 14080 Meth15_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-mcFlanksUpstream\n", " 12110 Meth15_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-mcFlanksUpstream\n", " 178405 Meth15_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-mcFlanksUpstream\n", " 204595 Meth15_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-mcFlanksUpstream\n", " 7279 Meth16_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-mcFlanksUpstream\n", " 5270 Meth16_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-mcFlanksUpstream\n", " 24942 Meth16_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-mcFlanksUpstream\n", " 37491 Meth16_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-mcFlanksUpstream\n", " 3164 Meth17_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-mcFlanksUpstream\n", " 1866 Meth17_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-mcFlanksUpstream\n", " 9531 Meth17_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-mcFlanksUpstream\n", " 14561 Meth17_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-mcFlanksUpstream\n", " 2202 Meth18_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-mcFlanksUpstream\n", " 1054 Meth18_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-mcFlanksUpstream\n", " 5987 Meth18_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-mcFlanksUpstream\n", " 9243 Meth18_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-mcFlanksUpstream\n", " 3588472 total\n" ] } ], "source": [ "#Count number of overlaps\n", "!wc -l *mcFlanksUpstream" ] }, { "cell_type": "code", "execution_count": 134, "metadata": { "collapsed": true }, "outputs": [], "source": [ "!wc -l *mcFlanksUpstream > Mcap-5x-mcFlanksUpstream-counts.txt" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "#### 4g. Downstream flanking regions" ] }, { "cell_type": "code", "execution_count": 135, "metadata": { "collapsed": false, "scrolled": true }, "outputs": [], "source": [ "%%bash\n", "\n", "for f in *bed\n", "do\n", " /usr/local/bin/intersectBed \\\n", " -u \\\n", " -a ${f} \\\n", " -b ../../../genome-feature-files/Mcap.GFFannotation.flanks.Downstream.gff \\\n", " > ${f}-mcFlanksDownstream\n", "done" ] }, { "cell_type": "code", "execution_count": 136, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "==> Meth10_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-mcFlanksDownstream <==\r\n", "1\t443126\t443128\t60.000000\r\n", "1\t1392759\t1392761\t50.000000\r\n", "1\t1392780\t1392782\t57.142857\r\n", "1\t1392793\t1392795\t57.142857\r\n", "1\t1392832\t1392834\t66.666667\r\n", "1\t1392838\t1392840\t60.000000\r\n", "1\t1392908\t1392910\t60.000000\r\n", "1\t1392921\t1392923\t60.000000\r\n", "1\t1396199\t1396201\t60.000000\r\n", "1\t1426748\t1426750\t100.000000\r\n", "\r\n", "==> Meth10_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-mcFlanksDownstream <==\r\n", "1\t150099\t150101\t40.000000\r\n", "1\t185808\t185810\t20.000000\r\n", "1\t185814\t185816\t20.000000\r\n", "1\t185830\t185832\t20.000000\r\n", "1\t185844\t185846\t16.666667\r\n", "1\t185868\t185870\t16.666667\r\n", "1\t185879\t185881\t14.285714\r\n", "1\t187123\t187125\t20.000000\r\n", "1\t217428\t217430\t20.000000\r\n", "1\t307046\t307048\t12.500000\r\n", "\r\n", "==> Meth10_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-mcFlanksDownstream <==\r\n", "1\t129421\t129423\t0.000000\r\n", "1\t129423\t129425\t0.000000\r\n", "1\t129446\t129448\t0.000000\r\n", "1\t129466\t129468\t0.000000\r\n", "1\t129480\t129482\t0.000000\r\n", "1\t129486\t129488\t0.000000\r\n", "1\t129495\t129497\t0.000000\r\n", "1\t129509\t129511\t0.000000\r\n", "1\t150075\t150077\t0.000000\r\n", "1\t150108\t150110\t0.000000\r\n", "\r\n", "==> Meth10_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-mcFlanksDownstream <==\r\n", "1\t129421\t129423\t0.000000\r\n", "1\t129423\t129425\t0.000000\r\n", "1\t129446\t129448\t0.000000\r\n", "1\t129466\t129468\t0.000000\r\n", "1\t129480\t129482\t0.000000\r\n", "1\t129486\t129488\t0.000000\r\n", "1\t129495\t129497\t0.000000\r\n", "1\t129509\t129511\t0.000000\r\n", "1\t150075\t150077\t0.000000\r\n", "1\t150099\t150101\t40.000000\r\n", "\r\n", "==> Meth11_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-mcFlanksDownstream <==\r\n", "1\t443126\t443128\t71.428571\r\n", "1\t788990\t788992\t60.000000\r\n", "1\t788995\t788997\t60.000000\r\n", "1\t1396199\t1396201\t55.555556\r\n", "1\t1426966\t1426968\t85.714286\r\n", "1\t1454029\t1454031\t88.888889\r\n", "1\t1454043\t1454045\t100.000000\r\n", "1\t1454631\t1454633\t100.000000\r\n", "1\t1454657\t1454659\t100.000000\r\n", "1\t1454715\t1454717\t83.333333\r\n", "\r\n", "==> Meth11_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-mcFlanksDownstream <==\r\n", "1\t217374\t217376\t16.666667\r\n", "1\t217399\t217401\t14.285714\r\n", "1\t307132\t307134\t20.000000\r\n", "1\t332179\t332181\t33.333333\r\n", "1\t332213\t332215\t20.000000\r\n", "1\t357091\t357093\t14.285714\r\n", "1\t357122\t357124\t16.666667\r\n", "1\t357397\t357399\t22.222222\r\n", "1\t404305\t404307\t20.000000\r\n", "1\t443089\t443091\t40.000000\r\n", "\r\n", "==> Meth11_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-mcFlanksDownstream <==\r\n", "1\t217269\t217271\t0.000000\r\n", "1\t217349\t217351\t0.000000\r\n", "1\t217355\t217357\t0.000000\r\n", "1\t217384\t217386\t0.000000\r\n", "1\t239744\t239746\t0.000000\r\n", "1\t239815\t239817\t0.000000\r\n", "1\t239831\t239833\t0.000000\r\n", "1\t239849\t239851\t0.000000\r\n", "1\t307128\t307130\t0.000000\r\n", "1\t307130\t307132\t0.000000\r\n", "\r\n", "==> Meth11_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-mcFlanksDownstream <==\r\n", "1\t217269\t217271\t0.000000\r\n", "1\t217349\t217351\t0.000000\r\n", "1\t217355\t217357\t0.000000\r\n", "1\t217374\t217376\t16.666667\r\n", "1\t217384\t217386\t0.000000\r\n", "1\t217399\t217401\t14.285714\r\n", "1\t239744\t239746\t0.000000\r\n", "1\t239815\t239817\t0.000000\r\n", "1\t239831\t239833\t0.000000\r\n", "1\t239849\t239851\t0.000000\r\n", "\r\n", "==> Meth12_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-mcFlanksDownstream <==\r\n", "1\t443089\t443091\t50.000000\r\n", "1\t443126\t443128\t50.000000\r\n", "1\t789333\t789335\t70.000000\r\n", "1\t1361040\t1361042\t100.000000\r\n", "1\t1361043\t1361045\t100.000000\r\n", "1\t1396199\t1396201\t80.000000\r\n", "1\t1425370\t1425372\t100.000000\r\n", "1\t1426944\t1426946\t100.000000\r\n", "1\t1426966\t1426968\t100.000000\r\n", "1\t1454029\t1454031\t100.000000\r\n", "\r\n", "==> Meth12_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-mcFlanksDownstream <==\r\n", "1\t21881\t21883\t16.666667\r\n", "1\t22117\t22119\t16.666667\r\n", "1\t52526\t52528\t20.000000\r\n", "1\t322694\t322696\t16.666667\r\n", "1\t331983\t331985\t16.666667\r\n", "1\t332024\t332026\t14.285714\r\n", "1\t352273\t352275\t11.111111\r\n", "1\t357391\t357393\t12.500000\r\n", "1\t360799\t360801\t16.666667\r\n", "1\t361490\t361492\t20.000000\r\n", "\r\n", "==> Meth12_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-mcFlanksDownstream <==\r\n", "1\t17709\t17711\t0.000000\r\n", "1\t17723\t17725\t0.000000\r\n", "1\t21734\t21736\t0.000000\r\n", "1\t21739\t21741\t0.000000\r\n", "1\t21757\t21759\t0.000000\r\n", "1\t21830\t21832\t0.000000\r\n", "1\t21840\t21842\t0.000000\r\n", "1\t22106\t22108\t0.000000\r\n", "1\t22111\t22113\t0.000000\r\n", "1\t22165\t22167\t0.000000\r\n", "\r\n", "==> Meth12_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-mcFlanksDownstream <==\r\n", "1\t17709\t17711\t0.000000\r\n", "1\t17723\t17725\t0.000000\r\n", "1\t21734\t21736\t0.000000\r\n", "1\t21739\t21741\t0.000000\r\n", "1\t21757\t21759\t0.000000\r\n", "1\t21830\t21832\t0.000000\r\n", "1\t21840\t21842\t0.000000\r\n", "1\t21881\t21883\t16.666667\r\n", "1\t22106\t22108\t0.000000\r\n", "1\t22111\t22113\t0.000000\r\n", "\r\n", "==> Meth13_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-mcFlanksDownstream <==\r\n", "1\t788995\t788997\t80.000000\r\n", "1\t1501390\t1501392\t94.642857\r\n", "1\t1501624\t1501626\t96.428571\r\n", "1\t1726224\t1726226\t96.875000\r\n", "1\t1726417\t1726419\t91.549296\r\n", "1\t1726438\t1726440\t100.000000\r\n", "1\t1774138\t1774140\t100.000000\r\n", "1\t1774296\t1774298\t100.000000\r\n", "1\t1874407\t1874409\t90.000000\r\n", "1\t1874414\t1874416\t100.000000\r\n", "\r\n", "==> Meth13_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-mcFlanksDownstream <==\r\n", "1\t21739\t21741\t13.636364\r\n", "1\t322944\t322946\t13.333333\r\n", "1\t580358\t580360\t14.594595\r\n", "1\t602056\t602058\t10.810811\r\n", "1\t701623\t701625\t16.129032\r\n", "1\t1774164\t1774166\t18.181818\r\n", "1\t1937990\t1937992\t18.181818\r\n", "1\t1938057\t1938059\t18.181818\r\n", "1\t2255941\t2255943\t45.238095\r\n", "2\t197130\t197132\t20.000000\r\n", "\r\n", "==> Meth13_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-mcFlanksDownstream <==\r\n", "1\t21757\t21759\t0.000000\r\n", "1\t21830\t21832\t0.000000\r\n", "1\t21840\t21842\t0.000000\r\n", "1\t21881\t21883\t6.666667\r\n", "1\t21967\t21969\t0.000000\r\n", "1\t21980\t21982\t0.000000\r\n", "1\t22008\t22010\t0.000000\r\n", "1\t22089\t22091\t0.000000\r\n", "1\t22106\t22108\t4.444444\r\n", "1\t22111\t22113\t5.882353\r\n", "\r\n", "==> Meth13_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-mcFlanksDownstream <==\r\n", "1\t21739\t21741\t13.636364\r\n", "1\t21757\t21759\t0.000000\r\n", "1\t21830\t21832\t0.000000\r\n", "1\t21840\t21842\t0.000000\r\n", "1\t21881\t21883\t6.666667\r\n", "1\t21967\t21969\t0.000000\r\n", "1\t21980\t21982\t0.000000\r\n", "1\t22008\t22010\t0.000000\r\n", "1\t22089\t22091\t0.000000\r\n", "1\t22106\t22108\t4.444444\r\n", "\r\n", "==> Meth14_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-mcFlanksDownstream <==\r\n", "1\t1726224\t1726226\t100.000000\r\n", "1\t1726417\t1726419\t93.589744\r\n", "1\t1726438\t1726440\t100.000000\r\n", "1\t1874454\t1874456\t90.740741\r\n", "1\t1882718\t1882720\t89.285714\r\n", "1\t1882722\t1882724\t92.857143\r\n", "1\t1882729\t1882731\t100.000000\r\n", "1\t1882838\t1882840\t98.876404\r\n", "1\t1882849\t1882851\t98.684211\r\n", "1\t2230095\t2230097\t78.260870\r\n", "\r\n", "==> Meth14_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-mcFlanksDownstream <==\r\n", "1\t305489\t305491\t11.111111\r\n", "1\t357091\t357093\t12.500000\r\n", "1\t357382\t357384\t13.043478\r\n", "1\t634819\t634821\t10.638298\r\n", "1\t701549\t701551\t31.578947\r\n", "1\t743459\t743461\t21.739130\r\n", "1\t1026560\t1026562\t11.111111\r\n", "1\t1175900\t1175902\t25.000000\r\n", "1\t1924121\t1924123\t11.111111\r\n", "1\t1937889\t1937891\t22.222222\r\n", "\r\n", "==> Meth14_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-mcFlanksDownstream <==\r\n", "1\t305242\t305244\t8.000000\r\n", "1\t305317\t305319\t0.000000\r\n", "1\t305384\t305386\t0.000000\r\n", "1\t322012\t322014\t0.000000\r\n", "1\t322018\t322020\t0.378788\r\n", "1\t322027\t322029\t0.757576\r\n", "1\t322033\t322035\t6.106870\r\n", "1\t322808\t322810\t1.176471\r\n", "1\t322820\t322822\t0.000000\r\n", "1\t322834\t322836\t1.470588\r\n", "\r\n", "==> Meth14_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-mcFlanksDownstream <==\r\n", "1\t305242\t305244\t8.000000\r\n", "1\t305317\t305319\t0.000000\r\n", "1\t305384\t305386\t0.000000\r\n", "1\t305489\t305491\t11.111111\r\n", "1\t322012\t322014\t0.000000\r\n", "1\t322018\t322020\t0.378788\r\n", "1\t322027\t322029\t0.757576\r\n", "1\t322033\t322035\t6.106870\r\n", "1\t322808\t322810\t1.176471\r\n", "1\t322820\t322822\t0.000000\r\n", "\r\n", "==> Meth15_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-mcFlanksDownstream <==\r\n", "1\t1726224\t1726226\t97.222222\r\n", "1\t1726417\t1726419\t93.846154\r\n", "1\t1726438\t1726440\t88.571429\r\n", "1\t1774138\t1774140\t100.000000\r\n", "1\t1774164\t1774166\t70.000000\r\n", "1\t1774296\t1774298\t93.548387\r\n", "1\t1874315\t1874317\t83.333333\r\n", "1\t1874407\t1874409\t66.666667\r\n", "1\t1874414\t1874416\t100.000000\r\n", "1\t1874454\t1874456\t92.682927\r\n", "\r\n", "==> Meth15_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-mcFlanksDownstream <==\r\n", "1\t185844\t185846\t25.000000\r\n", "1\t186587\t186589\t25.000000\r\n", "1\t357419\t357421\t11.111111\r\n", "1\t357504\t357506\t37.500000\r\n", "1\t357548\t357550\t33.333333\r\n", "1\t683117\t683119\t40.000000\r\n", "1\t743430\t743432\t11.538462\r\n", "1\t743455\t743457\t18.897638\r\n", "1\t946452\t946454\t23.809524\r\n", "1\t1019035\t1019037\t10.135135\r\n", "\r\n", "==> Meth15_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-mcFlanksDownstream <==\r\n", "1\t149978\t149980\t5.882353\r\n", "1\t150001\t150003\t0.000000\r\n", "1\t150012\t150014\t0.000000\r\n", "1\t150030\t150032\t0.000000\r\n", "1\t150075\t150077\t0.000000\r\n", "1\t150099\t150101\t0.000000\r\n", "1\t150108\t150110\t0.000000\r\n", "1\t150220\t150222\t0.000000\r\n", "1\t150283\t150285\t2.272727\r\n", "1\t150297\t150299\t0.000000\r\n", "\r\n", "==> Meth15_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-mcFlanksDownstream <==\r\n", "1\t149978\t149980\t5.882353\r\n", "1\t150001\t150003\t0.000000\r\n", "1\t150012\t150014\t0.000000\r\n", "1\t150030\t150032\t0.000000\r\n", "1\t150075\t150077\t0.000000\r\n", "1\t150099\t150101\t0.000000\r\n", "1\t150108\t150110\t0.000000\r\n", "1\t150220\t150222\t0.000000\r\n", "1\t150283\t150285\t2.272727\r\n", "1\t150297\t150299\t0.000000\r\n", "\r\n", "==> Meth16_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-mcFlanksDownstream <==\r\n", "1\t789213\t789215\t60.000000\r\n", "1\t2070697\t2070699\t60.000000\r\n", "1\t2070732\t2070734\t80.000000\r\n", "2\t197311\t197313\t100.000000\r\n", "2\t197321\t197323\t100.000000\r\n", "2\t197327\t197329\t100.000000\r\n", "2\t330308\t330310\t85.714286\r\n", "2\t330327\t330329\t100.000000\r\n", "2\t330330\t330332\t100.000000\r\n", "2\t330347\t330349\t75.000000\r\n", "\r\n", "==> Meth16_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-mcFlanksDownstream <==\r\n", "1\t217198\t217200\t14.285714\r\n", "1\t458648\t458650\t20.000000\r\n", "1\t743459\t743461\t40.000000\r\n", "1\t789254\t789256\t16.666667\r\n", "1\t789277\t789279\t20.000000\r\n", "1\t1708805\t1708807\t20.000000\r\n", "1\t1709206\t1709208\t16.666667\r\n", "2\t722906\t722908\t14.285714\r\n", "2\t722953\t722955\t20.000000\r\n", "2\t887899\t887901\t16.666667\r\n", "\r\n", "==> Meth16_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-mcFlanksDownstream <==\r\n", "1\t217219\t217221\t0.000000\r\n", "1\t217248\t217250\t0.000000\r\n", "1\t217269\t217271\t0.000000\r\n", "1\t322944\t322946\t0.000000\r\n", "1\t322963\t322965\t0.000000\r\n", "1\t458552\t458554\t0.000000\r\n", "1\t458666\t458668\t0.000000\r\n", "1\t458703\t458705\t0.000000\r\n", "1\t458918\t458920\t0.000000\r\n", "1\t458933\t458935\t0.000000\r\n", "\r\n", "==> Meth16_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-mcFlanksDownstream <==\r\n", "1\t217198\t217200\t14.285714\r\n", "1\t217219\t217221\t0.000000\r\n", "1\t217248\t217250\t0.000000\r\n", "1\t217269\t217271\t0.000000\r\n", "1\t322944\t322946\t0.000000\r\n", "1\t322963\t322965\t0.000000\r\n", "1\t458552\t458554\t0.000000\r\n", "1\t458648\t458650\t20.000000\r\n", "1\t458666\t458668\t0.000000\r\n", "1\t458703\t458705\t0.000000\r\n", "\r\n", "==> Meth17_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-mcFlanksDownstream <==\r\n", "2\t2167886\t2167888\t66.666667\r\n", "2\t2167889\t2167891\t80.000000\r\n", "2\t2864686\t2864688\t100.000000\r\n", "2\t2864820\t2864822\t100.000000\r\n", "2\t2902728\t2902730\t87.500000\r\n", "2\t2902746\t2902748\t100.000000\r\n", "2\t2902764\t2902766\t100.000000\r\n", "2\t2902772\t2902774\t100.000000\r\n", "2\t2902811\t2902813\t100.000000\r\n", "2\t2902818\t2902820\t100.000000\r\n", "\r\n", "==> Meth17_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-mcFlanksDownstream <==\r\n", "1\t778795\t778797\t40.000000\r\n", "1\t2655894\t2655896\t16.666667\r\n", "1\t2724041\t2724043\t16.666667\r\n", "2\t961832\t961834\t16.666667\r\n", "2\t1069847\t1069849\t16.666667\r\n", "2\t1144746\t1144748\t28.571429\r\n", "2\t1144752\t1144754\t28.571429\r\n", "2\t1753305\t1753307\t16.666667\r\n", "2\t1753324\t1753326\t28.571429\r\n", "2\t1753334\t1753336\t28.571429\r\n", "\r\n", "==> Meth17_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-mcFlanksDownstream <==\r\n", "1\t778696\t778698\t0.000000\r\n", "1\t789056\t789058\t0.000000\r\n", "1\t1143020\t1143022\t0.000000\r\n", "1\t1143031\t1143033\t0.000000\r\n", "1\t1143039\t1143041\t0.000000\r\n", "1\t1143043\t1143045\t0.000000\r\n", "1\t1143094\t1143096\t0.000000\r\n", "1\t1143105\t1143107\t0.000000\r\n", "1\t1143120\t1143122\t0.000000\r\n", "1\t1166612\t1166614\t0.000000\r\n", "\r\n", "==> Meth17_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-mcFlanksDownstream <==\r\n", "1\t778696\t778698\t0.000000\r\n", "1\t778795\t778797\t40.000000\r\n", "1\t789056\t789058\t0.000000\r\n", "1\t1143020\t1143022\t0.000000\r\n", "1\t1143031\t1143033\t0.000000\r\n", "1\t1143039\t1143041\t0.000000\r\n", "1\t1143043\t1143045\t0.000000\r\n", "1\t1143094\t1143096\t0.000000\r\n", "1\t1143105\t1143107\t0.000000\r\n", "1\t1143120\t1143122\t0.000000\r\n", "\r\n", "==> Meth18_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-mcFlanksDownstream <==\r\n", "2\t260911\t260913\t60.000000\r\n", "2\t301621\t301623\t60.000000\r\n", "2\t330280\t330282\t80.000000\r\n", "2\t330291\t330293\t75.000000\r\n", "2\t330308\t330310\t100.000000\r\n", "2\t330327\t330329\t90.909091\r\n", "2\t330330\t330332\t100.000000\r\n", "2\t330347\t330349\t92.307692\r\n", "2\t330364\t330366\t91.666667\r\n", "2\t330370\t330372\t100.000000\r\n", "\r\n", "==> Meth18_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-mcFlanksDownstream <==\r\n", "1\t646162\t646164\t20.000000\r\n", "1\t1700903\t1700905\t14.285714\r\n", "1\t1700905\t1700907\t14.285714\r\n", "7\t505356\t505358\t40.000000\r\n", "7\t638852\t638854\t20.000000\r\n", "7\t853347\t853349\t14.285714\r\n", "7\t2027717\t2027719\t20.000000\r\n", "10\t732294\t732296\t44.444444\r\n", "10\t832252\t832254\t33.333333\r\n", "10\t1079949\t1079951\t42.857143\r\n", "\r\n", "==> Meth18_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-mcFlanksDownstream <==\r\n", "1\t458933\t458935\t0.000000\r\n", "1\t458950\t458952\t0.000000\r\n", "1\t585916\t585918\t0.000000\r\n", "1\t602056\t602058\t0.000000\r\n", "1\t1700830\t1700832\t0.000000\r\n", "1\t1700835\t1700837\t0.000000\r\n", "1\t1700840\t1700842\t0.000000\r\n", "1\t1700850\t1700852\t0.000000\r\n", "1\t1700858\t1700860\t0.000000\r\n", "1\t1700860\t1700862\t0.000000\r\n", "\r\n", "==> Meth18_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-mcFlanksDownstream <==\r\n", "1\t458933\t458935\t0.000000\r\n", "1\t458950\t458952\t0.000000\r\n", "1\t585916\t585918\t0.000000\r\n", "1\t602056\t602058\t0.000000\r\n", "1\t646162\t646164\t20.000000\r\n", "1\t1700830\t1700832\t0.000000\r\n", "1\t1700835\t1700837\t0.000000\r\n", "1\t1700840\t1700842\t0.000000\r\n", "1\t1700850\t1700852\t0.000000\r\n", "1\t1700858\t1700860\t0.000000\r\n" ] } ], "source": [ "#Check output\n", "!head *mcFlanksDownstream" ] }, { "cell_type": "code", "execution_count": 137, "metadata": { "collapsed": false, "scrolled": true }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ " 26191 Meth10_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-mcFlanksDownstream\n", " 34072 Meth10_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-mcFlanksDownstream\n", " 197719 Meth10_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-mcFlanksDownstream\n", " 257982 Meth10_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-mcFlanksDownstream\n", " 30692 Meth11_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-mcFlanksDownstream\n", " 32246 Meth11_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-mcFlanksDownstream\n", " 201955 Meth11_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-mcFlanksDownstream\n", " 264893 Meth11_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-mcFlanksDownstream\n", " 62551 Meth12_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-mcFlanksDownstream\n", " 60969 Meth12_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-mcFlanksDownstream\n", " 376813 Meth12_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-mcFlanksDownstream\n", " 500333 Meth12_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-mcFlanksDownstream\n", " 15109 Meth13_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-mcFlanksDownstream\n", " 9551 Meth13_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-mcFlanksDownstream\n", " 147647 Meth13_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-mcFlanksDownstream\n", " 172307 Meth13_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-mcFlanksDownstream\n", " 10555 Meth14_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-mcFlanksDownstream\n", " 8362 Meth14_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-mcFlanksDownstream\n", " 125021 Meth14_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-mcFlanksDownstream\n", " 143938 Meth14_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-mcFlanksDownstream\n", " 13204 Meth15_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-mcFlanksDownstream\n", " 11318 Meth15_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-mcFlanksDownstream\n", " 147484 Meth15_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-mcFlanksDownstream\n", " 172006 Meth15_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-mcFlanksDownstream\n", " 6970 Meth16_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-mcFlanksDownstream\n", " 4302 Meth16_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-mcFlanksDownstream\n", " 21381 Meth16_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-mcFlanksDownstream\n", " 32653 Meth16_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-mcFlanksDownstream\n", " 2901 Meth17_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-mcFlanksDownstream\n", " 1723 Meth17_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-mcFlanksDownstream\n", " 8364 Meth17_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-mcFlanksDownstream\n", " 12988 Meth17_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-mcFlanksDownstream\n", " 2124 Meth18_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-mcFlanksDownstream\n", " 884 Meth18_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-mcFlanksDownstream\n", " 5160 Meth18_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-mcFlanksDownstream\n", " 8168 Meth18_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-mcFlanksDownstream\n", " 3130536 total\n" ] } ], "source": [ "#Count number of overlaps\n", "!wc -l *mcFlanksDownstream" ] }, { "cell_type": "code", "execution_count": 138, "metadata": { "collapsed": false }, "outputs": [], "source": [ "!wc -l *mcFlanksDownstream > Mcap-5x-mcFlanksDownstream-counts.txt" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "#### 4h. Intergenic" ] }, { "cell_type": "code", "execution_count": 139, "metadata": { "collapsed": false }, "outputs": [], "source": [ "%%bash \n", "\n", "for f in *bed\n", "do\n", " /usr/local/bin/intersectBed \\\n", " -u \\\n", " -a ${f} \\\n", " -b ../../../genome-feature-files/Mcap.GFFannotation.intergenic.bed \\\n", " > ${f}-mcIntergenic\n", "done" ] }, { "cell_type": "code", "execution_count": 140, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "==> Meth10_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-mcIntergenic <==\n", "1\t320600\t320602\t66.666667\n", "1\t320631\t320633\t50.000000\n", "1\t446577\t446579\t80.000000\n", "1\t446641\t446643\t71.428571\n", "1\t446659\t446661\t71.428571\n", "1\t446682\t446684\t66.666667\n", "1\t446691\t446693\t80.000000\n", "1\t446746\t446748\t50.000000\n", "1\t448144\t448146\t76.923077\n", "1\t449627\t449629\t100.000000\n", "\n", "==> Meth10_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-mcIntergenic <==\n", "1\t140551\t140553\t33.333333\n", "1\t169735\t169737\t12.500000\n", "1\t169771\t169773\t42.857143\n", "1\t169796\t169798\t14.285714\n", "1\t169800\t169802\t16.666667\n", "1\t208981\t208983\t40.000000\n", "1\t211907\t211909\t16.666667\n", "1\t213057\t213059\t14.285714\n", "1\t213347\t213349\t14.285714\n", "1\t213738\t213740\t16.666667\n", "\n", "==> Meth10_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-mcIntergenic <==\n", "1\t6570\t6572\t0.000000\n", "1\t6713\t6715\t0.000000\n", "1\t6780\t6782\t0.000000\n", "1\t6813\t6815\t0.000000\n", "1\t6818\t6820\t0.000000\n", "1\t53668\t53670\t0.000000\n", "1\t129509\t129511\t0.000000\n", "1\t129522\t129524\t0.000000\n", "1\t140521\t140523\t0.000000\n", "1\t140545\t140547\t0.000000\n", "\n", "==> Meth10_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-mcIntergenic <==\n", "1\t6570\t6572\t0.000000\n", "1\t6713\t6715\t0.000000\n", "1\t6780\t6782\t0.000000\n", "1\t6813\t6815\t0.000000\n", "1\t6818\t6820\t0.000000\n", "1\t53668\t53670\t0.000000\n", "1\t129509\t129511\t0.000000\n", "1\t129522\t129524\t0.000000\n", "1\t140521\t140523\t0.000000\n", "1\t140545\t140547\t0.000000\n", "\n", "==> Meth11_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-mcIntergenic <==\n", "1\t6905\t6907\t60.000000\n", "1\t7273\t7275\t80.000000\n", "1\t446465\t446467\t50.000000\n", "1\t446472\t446474\t100.000000\n", "1\t446481\t446483\t83.333333\n", "1\t446577\t446579\t62.500000\n", "1\t446641\t446643\t100.000000\n", "1\t446659\t446661\t100.000000\n", "1\t446682\t446684\t100.000000\n", "1\t448144\t448146\t63.636364\n", "\n", "==> Meth11_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-mcIntergenic <==\n", "1\t6550\t6552\t12.500000\n", "1\t6671\t6673\t20.000000\n", "1\t6996\t6998\t20.000000\n", "1\t7016\t7018\t40.000000\n", "1\t7019\t7021\t40.000000\n", "1\t7293\t7295\t16.666667\n", "1\t7427\t7429\t16.666667\n", "1\t153767\t153769\t20.000000\n", "1\t193930\t193932\t20.000000\n", "1\t203231\t203233\t20.000000\n", "\n", "==> Meth11_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-mcIntergenic <==\n", "1\t4929\t4931\t0.000000\n", "1\t5665\t5667\t0.000000\n", "1\t6453\t6455\t0.000000\n", "1\t6484\t6486\t0.000000\n", "1\t6527\t6529\t0.000000\n", "1\t6570\t6572\t0.000000\n", "1\t6618\t6620\t0.000000\n", "1\t6652\t6654\t0.000000\n", "1\t6661\t6663\t0.000000\n", "1\t6668\t6670\t0.000000\n", "\n", "==> Meth11_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-mcIntergenic <==\n", "1\t4929\t4931\t0.000000\n", "1\t5665\t5667\t0.000000\n", "1\t6453\t6455\t0.000000\n", "1\t6484\t6486\t0.000000\n", "1\t6527\t6529\t0.000000\n", "1\t6550\t6552\t12.500000\n", "1\t6570\t6572\t0.000000\n", "1\t6618\t6620\t0.000000\n", "1\t6652\t6654\t0.000000\n", "1\t6661\t6663\t0.000000\n", "\n", "==> Meth12_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-mcIntergenic <==\n", "1\t4948\t4950\t50.000000\n", "1\t4967\t4969\t50.000000\n", "1\t4986\t4988\t50.000000\n", "1\t57065\t57067\t80.000000\n", "1\t446150\t446152\t80.000000\n", "1\t446157\t446159\t60.000000\n", "1\t446262\t446264\t66.666667\n", "1\t446271\t446273\t66.666667\n", "1\t446344\t446346\t62.500000\n", "1\t446367\t446369\t66.666667\n", "\n", "==> Meth12_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-mcIntergenic <==\n", "1\t4190\t4192\t16.666667\n", "1\t4891\t4893\t33.333333\n", "1\t4910\t4912\t28.571429\n", "1\t4929\t4931\t33.333333\n", "1\t5005\t5007\t28.571429\n", "1\t5024\t5026\t40.000000\n", "1\t5151\t5153\t20.000000\n", "1\t5160\t5162\t16.666667\n", "1\t5228\t5230\t11.111111\n", "1\t6282\t6284\t11.111111\n", "\n", "==> Meth12_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-mcIntergenic <==\n", "1\t4062\t4064\t0.000000\n", "1\t4069\t4071\t0.000000\n", "1\t4077\t4079\t0.000000\n", "1\t4086\t4088\t0.000000\n", "1\t4146\t4148\t0.000000\n", "1\t4150\t4152\t0.000000\n", "1\t4155\t4157\t0.000000\n", "1\t4172\t4174\t0.000000\n", "1\t4184\t4186\t0.000000\n", "1\t5043\t5045\t0.000000\n", "\n", "==> Meth12_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-mcIntergenic <==\n", "1\t4062\t4064\t0.000000\n", "1\t4069\t4071\t0.000000\n", "1\t4077\t4079\t0.000000\n", "1\t4086\t4088\t0.000000\n", "1\t4146\t4148\t0.000000\n", "1\t4150\t4152\t0.000000\n", "1\t4155\t4157\t0.000000\n", "1\t4172\t4174\t0.000000\n", "1\t4184\t4186\t0.000000\n", "1\t4190\t4192\t16.666667\n", "\n", "==> Meth13_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-mcIntergenic <==\n", "1\t274922\t274924\t92.307692\n", "1\t274940\t274942\t92.307692\n", "1\t275004\t275006\t92.307692\n", "1\t275006\t275008\t92.307692\n", "1\t275047\t275049\t92.307692\n", "1\t275056\t275058\t92.307692\n", "1\t275058\t275060\t92.307692\n", "1\t275072\t275074\t92.307692\n", "1\t275074\t275076\t92.307692\n", "1\t275084\t275086\t92.307692\n", "\n", "==> Meth13_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-mcIntergenic <==\n", "1\t15092\t15094\t30.000000\n", "1\t34139\t34141\t11.764706\n", "1\t169847\t169849\t12.820513\n", "1\t198078\t198080\t30.434783\n", "1\t203991\t203993\t12.500000\n", "1\t227400\t227402\t18.750000\n", "1\t227407\t227409\t17.187500\n", "1\t227416\t227418\t13.953488\n", "1\t241592\t241594\t14.545455\n", "1\t255850\t255852\t40.625000\n", "\n", "==> Meth13_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-mcIntergenic <==\n", "1\t3493\t3495\t0.000000\n", "1\t3518\t3520\t0.000000\n", "1\t3727\t3729\t0.000000\n", "1\t3752\t3754\t0.000000\n", "1\t3757\t3759\t0.000000\n", "1\t3770\t3772\t0.000000\n", "1\t11979\t11981\t0.000000\n", "1\t11985\t11987\t0.000000\n", "1\t11994\t11996\t0.000000\n", "1\t12043\t12045\t0.000000\n", "\n", "==> Meth13_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-mcIntergenic <==\n", "1\t3493\t3495\t0.000000\n", "1\t3518\t3520\t0.000000\n", "1\t3727\t3729\t0.000000\n", "1\t3752\t3754\t0.000000\n", "1\t3757\t3759\t0.000000\n", "1\t3770\t3772\t0.000000\n", "1\t11979\t11981\t0.000000\n", "1\t11985\t11987\t0.000000\n", "1\t11994\t11996\t0.000000\n", "1\t12043\t12045\t0.000000\n", "\n", "==> Meth14_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-mcIntergenic <==\n", "1\t32228\t32230\t100.000000\n", "1\t246227\t246229\t100.000000\n", "1\t317029\t317031\t100.000000\n", "1\t451094\t451096\t100.000000\n", "1\t455318\t455320\t60.000000\n", "1\t455610\t455612\t100.000000\n", "1\t616272\t616274\t57.142857\n", "1\t926227\t926229\t100.000000\n", "1\t926244\t926246\t95.000000\n", "1\t926302\t926304\t72.500000\n", "\n", "==> Meth14_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-mcIntergenic <==\n", "1\t166013\t166015\t12.500000\n", "1\t227400\t227402\t11.200000\n", "1\t230854\t230856\t14.285714\n", "1\t246955\t246957\t29.545455\n", "1\t248898\t248900\t13.333333\n", "1\t249322\t249324\t42.857143\n", "1\t257203\t257205\t14.285714\n", "1\t309954\t309956\t10.526316\n", "1\t314160\t314162\t32.352941\n", "1\t314207\t314209\t16.666667\n", "\n", "==> Meth14_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-mcIntergenic <==\n", "1\t3727\t3729\t0.000000\n", "1\t3752\t3754\t0.000000\n", "1\t3757\t3759\t0.000000\n", "1\t3770\t3772\t0.000000\n", "1\t11876\t11878\t0.000000\n", "1\t11887\t11889\t0.000000\n", "1\t11894\t11896\t0.000000\n", "1\t11941\t11943\t0.000000\n", "1\t11954\t11956\t0.000000\n", "1\t11975\t11977\t0.000000\n", "\n", "==> Meth14_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-mcIntergenic <==\n", "1\t3727\t3729\t0.000000\n", "1\t3752\t3754\t0.000000\n", "1\t3757\t3759\t0.000000\n", "1\t3770\t3772\t0.000000\n", "1\t11876\t11878\t0.000000\n", "1\t11887\t11889\t0.000000\n", "1\t11894\t11896\t0.000000\n", "1\t11941\t11943\t0.000000\n", "1\t11954\t11956\t0.000000\n", "1\t11975\t11977\t0.000000\n", "\n", "==> Meth15_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-mcIntergenic <==\n", "1\t130507\t130509\t90.000000\n", "1\t241717\t241719\t100.000000\n", "1\t241722\t241724\t100.000000\n", "1\t246227\t246229\t100.000000\n", "1\t317029\t317031\t100.000000\n", "1\t384618\t384620\t100.000000\n", "1\t415808\t415810\t50.000000\n", "1\t474458\t474460\t50.000000\n", "1\t594989\t594991\t66.666667\n", "1\t615972\t615974\t73.333333\n", "\n", "==> Meth15_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-mcIntergenic <==\n", "1\t169847\t169849\t14.285714\n", "1\t169891\t169893\t11.428571\n", "1\t169927\t169929\t20.000000\n", "1\t169936\t169938\t22.857143\n", "1\t170062\t170064\t21.052632\n", "1\t170097\t170099\t22.857143\n", "1\t170127\t170129\t22.857143\n", "1\t170144\t170146\t22.857143\n", "1\t170176\t170178\t22.857143\n", "1\t170211\t170213\t28.571429\n", "\n", "==> Meth15_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-mcIntergenic <==\n", "1\t3493\t3495\t0.000000\n", "1\t3518\t3520\t0.000000\n", "1\t3727\t3729\t8.695652\n", "1\t3752\t3754\t0.000000\n", "1\t3757\t3759\t0.000000\n", "1\t3770\t3772\t0.000000\n", "1\t29753\t29755\t3.200000\n", "1\t29821\t29823\t7.086614\n", "1\t32243\t32245\t1.388889\n", "1\t32283\t32285\t0.000000\n", "\n", "==> Meth15_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-mcIntergenic <==\n", "1\t3493\t3495\t0.000000\n", "1\t3518\t3520\t0.000000\n", "1\t3727\t3729\t8.695652\n", "1\t3752\t3754\t0.000000\n", "1\t3757\t3759\t0.000000\n", "1\t3770\t3772\t0.000000\n", "1\t29753\t29755\t3.200000\n", "1\t29821\t29823\t7.086614\n", "1\t32243\t32245\t1.388889\n", "1\t32283\t32285\t0.000000\n", "\n", "==> Meth16_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-mcIntergenic <==\n", "1\t446326\t446328\t80.000000\n", "1\t446344\t446346\t100.000000\n", "1\t446367\t446369\t100.000000\n", "1\t446376\t446378\t100.000000\n", "1\t1006917\t1006919\t60.000000\n", "1\t1006924\t1006926\t60.000000\n", "1\t1663145\t1663147\t60.000000\n", "1\t1747883\t1747885\t50.000000\n", "1\t2069304\t2069306\t66.666667\n", "1\t2069317\t2069319\t71.428571\n", "\n", "==> Meth16_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-mcIntergenic <==\n", "1\t211907\t211909\t40.000000\n", "1\t234158\t234160\t14.285714\n", "1\t234196\t234198\t12.500000\n", "1\t244563\t244565\t20.000000\n", "1\t269174\t269176\t16.666667\n", "1\t269178\t269180\t16.666667\n", "1\t269182\t269184\t16.666667\n", "1\t284269\t284271\t16.666667\n", "1\t378640\t378642\t20.000000\n", "1\t387734\t387736\t20.000000\n", "\n", "==> Meth16_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-mcIntergenic <==\n", "1\t5228\t5230\t0.000000\n", "1\t5243\t5245\t0.000000\n", "1\t5247\t5249\t0.000000\n", "1\t5296\t5298\t0.000000\n", "1\t192753\t192755\t0.000000\n", "1\t211905\t211907\t0.000000\n", "1\t211917\t211919\t0.000000\n", "1\t211925\t211927\t0.000000\n", "1\t213276\t213278\t0.000000\n", "1\t213738\t213740\t0.000000\n", "\n", "==> Meth16_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-mcIntergenic <==\n", "1\t5228\t5230\t0.000000\n", "1\t5243\t5245\t0.000000\n", "1\t5247\t5249\t0.000000\n", "1\t5296\t5298\t0.000000\n", "1\t192753\t192755\t0.000000\n", "1\t211905\t211907\t0.000000\n", "1\t211907\t211909\t40.000000\n", "1\t211917\t211919\t0.000000\n", "1\t211925\t211927\t0.000000\n", "1\t213276\t213278\t0.000000\n", "\n", "==> Meth17_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-mcIntergenic <==\n", "1\t2069317\t2069319\t80.000000\n", "1\t2069442\t2069444\t100.000000\n", "1\t2069451\t2069453\t100.000000\n", "1\t2069519\t2069521\t60.000000\n", "1\t2132954\t2132956\t100.000000\n", "1\t2133389\t2133391\t66.666667\n", "1\t2133406\t2133408\t66.666667\n", "1\t2133409\t2133411\t66.666667\n", "1\t2203066\t2203068\t85.714286\n", "1\t2203090\t2203092\t100.000000\n", "\n", "==> Meth17_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-mcIntergenic <==\n", "1\t460920\t460922\t40.000000\n", "1\t460947\t460949\t33.333333\n", "1\t460953\t460955\t33.333333\n", "1\t461051\t461053\t20.000000\n", "1\t519486\t519488\t28.571429\n", "1\t519505\t519507\t33.333333\n", "1\t716952\t716954\t33.333333\n", "1\t787841\t787843\t40.000000\n", "1\t787844\t787846\t40.000000\n", "1\t788249\t788251\t20.000000\n", "\n", "==> Meth17_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-mcIntergenic <==\n", "1\t210921\t210923\t0.000000\n", "1\t210930\t210932\t0.000000\n", "1\t219905\t219907\t0.000000\n", "1\t229825\t229827\t0.000000\n", "1\t229852\t229854\t0.000000\n", "1\t231344\t231346\t0.000000\n", "1\t233876\t233878\t0.000000\n", "1\t233894\t233896\t0.000000\n", "1\t255402\t255404\t0.000000\n", "1\t271124\t271126\t0.000000\n", "\n", "==> Meth17_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-mcIntergenic <==\n", "1\t210921\t210923\t0.000000\n", "1\t210930\t210932\t0.000000\n", "1\t219905\t219907\t0.000000\n", "1\t229825\t229827\t0.000000\n", "1\t229852\t229854\t0.000000\n", "1\t231344\t231346\t0.000000\n", "1\t233876\t233878\t0.000000\n", "1\t233894\t233896\t0.000000\n", "1\t255402\t255404\t0.000000\n", "1\t271124\t271126\t0.000000\n", "\n", "==> Meth18_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-mcIntergenic <==\n", "1\t1002973\t1002975\t50.000000\n", "1\t1343240\t1343242\t100.000000\n", "1\t1343249\t1343251\t100.000000\n", "1\t1343263\t1343265\t83.333333\n", "1\t1343265\t1343267\t100.000000\n", "1\t1343295\t1343297\t100.000000\n", "1\t1343304\t1343306\t100.000000\n", "1\t1343320\t1343322\t100.000000\n", "1\t1451821\t1451823\t60.000000\n", "1\t1747972\t1747974\t80.000000\n", "\n", "==> Meth18_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-mcIntergenic <==\n", "1\t8113\t8115\t20.000000\n", "1\t277994\t277996\t16.666667\n", "1\t387294\t387296\t20.000000\n", "1\t461787\t461789\t40.000000\n", "1\t605019\t605021\t28.571429\n", "1\t605050\t605052\t33.333333\n", "1\t807639\t807641\t20.000000\n", "1\t994107\t994109\t40.000000\n", "1\t1061927\t1061929\t20.000000\n", "1\t1061967\t1061969\t20.000000\n", "\n", "==> Meth18_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-mcIntergenic <==\n", "1\t224609\t224611\t0.000000\n", "1\t264560\t264562\t0.000000\n", "1\t264598\t264600\t0.000000\n", "1\t271145\t271147\t0.000000\n", "1\t278004\t278006\t0.000000\n", "1\t278039\t278041\t0.000000\n", "1\t278049\t278051\t0.000000\n", "1\t278067\t278069\t0.000000\n", "1\t280413\t280415\t0.000000\n", "1\t280448\t280450\t0.000000\n", "\n", "==> Meth18_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-mcIntergenic <==\n", "1\t8113\t8115\t20.000000\n", "1\t224609\t224611\t0.000000\n", "1\t264560\t264562\t0.000000\n", "1\t264598\t264600\t0.000000\n", "1\t271145\t271147\t0.000000\n", "1\t277994\t277996\t16.666667\n", "1\t278004\t278006\t0.000000\n", "1\t278039\t278041\t0.000000\n", "1\t278049\t278051\t0.000000\n", "1\t278067\t278069\t0.000000\n" ] } ], "source": [ "#Check output\n", "!head *mcIntergenic" ] }, { "cell_type": "code", "execution_count": 141, "metadata": { "collapsed": false, "scrolled": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ " 102964 Meth10_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-mcIntergenic\n", " 223838 Meth10_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-mcIntergenic\n", " 1540576 Meth10_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-mcIntergenic\n", " 1867378 Meth10_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-mcIntergenic\n", " 124280 Meth11_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-mcIntergenic\n", " 207392 Meth11_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-mcIntergenic\n", " 1540755 Meth11_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-mcIntergenic\n", " 1872427 Meth11_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-mcIntergenic\n", " 253319 Meth12_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-mcIntergenic\n", " 422423 Meth12_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-mcIntergenic\n", " 2932087 Meth12_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-mcIntergenic\n", " 3607829 Meth12_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-mcIntergenic\n", " 70019 Meth13_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-mcIntergenic\n", " 63933 Meth13_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-mcIntergenic\n", " 1291068 Meth13_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-mcIntergenic\n", " 1425020 Meth13_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-mcIntergenic\n", " 49667 Meth14_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-mcIntergenic\n", " 54910 Meth14_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-mcIntergenic\n", " 1078224 Meth14_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-mcIntergenic\n", " 1182801 Meth14_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-mcIntergenic\n", " 61587 Meth15_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-mcIntergenic\n", " 74392 Meth15_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-mcIntergenic\n", " 1295768 Meth15_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-mcIntergenic\n", " 1431747 Meth15_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-mcIntergenic\n", " 30278 Meth16_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-mcIntergenic\n", " 32744 Meth16_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-mcIntergenic\n", " 182381 Meth16_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-mcIntergenic\n", " 245403 Meth16_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-mcIntergenic\n", " 13146 Meth17_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-mcIntergenic\n", " 13262 Meth17_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-mcIntergenic\n", " 81639 Meth17_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-mcIntergenic\n", " 108047 Meth17_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-mcIntergenic\n", " 8945 Meth18_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-mcIntergenic\n", " 8517 Meth18_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-mcIntergenic\n", " 53523 Meth18_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-mcIntergenic\n", " 70985 Meth18_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-mcIntergenic\n", " 23623274 total\n" ] } ], "source": [ "#Count number of overlaps\n", "!wc -l *mcIntergenic" ] }, { "cell_type": "code", "execution_count": 142, "metadata": { "collapsed": true }, "outputs": [], "source": [ "!wc -l *mcIntergenic > Mcap-5x-mcIntergenic-counts.txt" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "## *P. acuta*" ] }, { "cell_type": "code", "execution_count": 143, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "/Users/yaamini/Documents/Meth_Compare/analyses/Characterizing-CpG-Methylation-5x\n" ] } ], "source": [ "cd .." ] }, { "cell_type": "code", "execution_count": 144, "metadata": { "collapsed": true }, "outputs": [], "source": [ "#Make a directory for Pact output\n", "#!mkdir Pact" ] }, { "cell_type": "code", "execution_count": 145, "metadata": { "collapsed": false, "scrolled": true }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "/Users/yaamini/Documents/Meth_Compare/analyses/Characterizing-CpG-Methylation-5x/Pact\n" ] } ], "source": [ "cd Pact/" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "### 1. Characterize CG motif locations in feature tracks" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "#### 1a. Set variable paths" ] }, { "cell_type": "code", "execution_count": 146, "metadata": { "collapsed": true }, "outputs": [], "source": [ "paGenes = \"../../../genome-feature-files/Pact.GFFannotation.Genes.gff\"" ] }, { "cell_type": "code", "execution_count": 147, "metadata": { "collapsed": true }, "outputs": [], "source": [ "paCDS = \"../../../genome-feature-files/Pact.GFFannotation.CDS.gff\"" ] }, { "cell_type": "code", "execution_count": 148, "metadata": { "collapsed": true }, "outputs": [], "source": [ "paIntron = \"../../../genome-feature-files/Pact.GFFannotation.Intron.gff\"" ] }, { "cell_type": "code", "execution_count": 149, "metadata": { "collapsed": true }, "outputs": [], "source": [ "paFlanks = \"../../../genome-feature-files/Pact.GFFannotation.flanks.gff\"" ] }, { "cell_type": "code", "execution_count": 150, "metadata": { "collapsed": true }, "outputs": [], "source": [ "paUpstream = \"../../../genome-feature-files/Pact.GFFannotation.flanks.Upstream.gff\"" ] }, { "cell_type": "code", "execution_count": 151, "metadata": { "collapsed": true }, "outputs": [], "source": [ "paDownstream = \"../../../genome-feature-files/Pact.GFFannotation.flanks.Downstream.gff\"" ] }, { "cell_type": "code", "execution_count": 152, "metadata": { "collapsed": true }, "outputs": [], "source": [ "paIntergenic = \"../../../genome-feature-files/Pact.GFFannotation.intergenic.bed\"" ] }, { "cell_type": "code", "execution_count": 153, "metadata": { "collapsed": true }, "outputs": [], "source": [ "paCGMotifs = \"../../../genome-feature-files/Pact_CpG.gff\"" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "#### 1b. Check variable paths" ] }, { "cell_type": "code", "execution_count": 154, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "scaffold6_cov64\tAUGUSTUS\tgene\t1\t5652\t0.46\t-\t.\tg1\n", "scaffold6_cov64\tAUGUSTUS\tgene\t5805\t6678\t0.57\t+\t.\tg2\n", "scaffold7_cov100\tAUGUSTUS\tgene\t1\t2566\t0.96\t+\t.\tg3\n", "scaffold7_cov100\tAUGUSTUS\tgene\t3467\t6217\t0.78\t-\t.\tg4\n", "scaffold7_cov100\tAUGUSTUS\tgene\t7069\t9073\t1\t-\t.\tg5\n", "scaffold7_cov100\tAUGUSTUS\tgene\t9590\t11670\t0.8\t-\t.\tg6\n", "scaffold7_cov100\tAUGUSTUS\tgene\t13339\t15463\t0.92\t-\t.\tg7\n", "scaffold7_cov100\tAUGUSTUS\tgene\t15738\t18320\t0.96\t+\t.\tg8\n", "scaffold7_cov100\tAUGUSTUS\tgene\t18586\t19270\t0.99\t-\t.\tg9\n", "scaffold7_cov100\tAUGUSTUS\tgene\t19312\t20050\t0.74\t+\t.\tg10\n", " 64558 ../../../genome-feature-files/Pact.GFFannotation.Genes.gff\n" ] } ], "source": [ "!head {paGenes}\n", "!wc -l {paGenes}" ] }, { "cell_type": "code", "execution_count": 155, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "scaffold6_cov64\tAUGUSTUS\tCDS\t495\t842\t0.84\t-\t2\ttranscript_id \"g1.t1\"; gene_id \"g1\";\n", "scaffold6_cov64\tAUGUSTUS\tCDS\t1208\t1555\t0.92\t-\t2\ttranscript_id \"g1.t1\"; gene_id \"g1\";\n", "scaffold6_cov64\tAUGUSTUS\tCDS\t1922\t2269\t1\t-\t2\ttranscript_id \"g1.t1\"; gene_id \"g1\";\n", "scaffold6_cov64\tAUGUSTUS\tCDS\t5583\t5652\t0.26\t-\t0\ttranscript_id \"g1.t1\"; gene_id \"g1\";\n", "scaffold6_cov64\tAUGUSTUS\tCDS\t495\t842\t0.84\t-\t2\ttranscript_id \"g1.t2\"; gene_id \"g1\";\n", "scaffold6_cov64\tAUGUSTUS\tCDS\t1208\t1555\t0.92\t-\t2\ttranscript_id \"g1.t2\"; gene_id \"g1\";\n", "scaffold6_cov64\tAUGUSTUS\tCDS\t1922\t2269\t1\t-\t2\ttranscript_id \"g1.t2\"; gene_id \"g1\";\n", "scaffold6_cov64\tAUGUSTUS\tCDS\t4754\t4851\t0.4\t-\t1\ttranscript_id \"g1.t2\"; gene_id \"g1\";\n", "scaffold6_cov64\tAUGUSTUS\tCDS\t5594\t5652\t0.54\t-\t0\ttranscript_id \"g1.t2\"; gene_id \"g1\";\n", "scaffold6_cov64\tAUGUSTUS\tCDS\t5805\t5838\t0.98\t+\t0\ttranscript_id \"g2.t1\"; gene_id \"g2\";\n", " 318484 ../../../genome-feature-files/Pact.GFFannotation.CDS.gff\n" ] } ], "source": [ "!head {paCDS}\n", "!wc -l {paCDS}" ] }, { "cell_type": "code", "execution_count": 156, "metadata": { "collapsed": false, "scrolled": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "scaffold6_cov64\tAUGUSTUS\tintron\t1\t494\t0.82\t-\t.\ttranscript_id \"g1.t1\"; gene_id \"g1\";\n", "scaffold6_cov64\tAUGUSTUS\tintron\t843\t1207\t0.92\t-\t.\ttranscript_id \"g1.t1\"; gene_id \"g1\";\n", "scaffold6_cov64\tAUGUSTUS\tintron\t1556\t1921\t1\t-\t.\ttranscript_id \"g1.t1\"; gene_id \"g1\";\n", "scaffold6_cov64\tAUGUSTUS\tintron\t2270\t5582\t0.23\t-\t.\ttranscript_id \"g1.t1\"; gene_id \"g1\";\n", "scaffold6_cov64\tAUGUSTUS\tintron\t1\t494\t0.82\t-\t.\ttranscript_id \"g1.t2\"; gene_id \"g1\";\n", "scaffold6_cov64\tAUGUSTUS\tintron\t843\t1207\t0.92\t-\t.\ttranscript_id \"g1.t2\"; gene_id \"g1\";\n", "scaffold6_cov64\tAUGUSTUS\tintron\t1556\t1921\t1\t-\t.\ttranscript_id \"g1.t2\"; gene_id \"g1\";\n", "scaffold6_cov64\tAUGUSTUS\tintron\t2270\t4753\t0.4\t-\t.\ttranscript_id \"g1.t2\"; gene_id \"g1\";\n", "scaffold6_cov64\tAUGUSTUS\tintron\t4852\t5593\t0.48\t-\t.\ttranscript_id \"g1.t2\"; gene_id \"g1\";\n", "scaffold6_cov64\tAUGUSTUS\tintron\t5839\t5945\t0.54\t+\t.\ttranscript_id \"g2.t1\"; gene_id \"g2\";\n", " 241534 ../../../genome-feature-files/Pact.GFFannotation.Intron.gff\n" ] } ], "source": [ "!head {paIntron}\n", "!wc -l {paIntron}" ] }, { "cell_type": "code", "execution_count": 157, "metadata": { "collapsed": false, "scrolled": true }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "scaffold6_cov64\tAUGUSTUS\tgene\t5653\t5804\t0.46\t-\t.\tg1\n", "scaffold6_cov64\tAUGUSTUS\tgene\t5653\t5804\t0.57\t+\t.\tg2\n", "scaffold6_cov64\tAUGUSTUS\tgene\t6679\t7678\t0.57\t+\t.\tg2\n", "scaffold7_cov100\tAUGUSTUS\tgene\t2567\t3466\t0.96\t+\t.\tg3\n", "scaffold7_cov100\tAUGUSTUS\tgene\t2567\t3466\t0.78\t-\t.\tg4\n", "scaffold7_cov100\tAUGUSTUS\tgene\t6218\t7068\t0.78\t-\t.\tg4\n", "scaffold7_cov100\tAUGUSTUS\tgene\t6218\t7068\t1\t-\t.\tg5\n", "scaffold7_cov100\tAUGUSTUS\tgene\t9074\t9589\t1\t-\t.\tg5\n", "scaffold7_cov100\tAUGUSTUS\tgene\t9074\t9589\t0.8\t-\t.\tg6\n", "scaffold7_cov100\tAUGUSTUS\tgene\t11671\t12670\t0.8\t-\t.\tg6\n", " 143874 ../../../genome-feature-files/Pact.GFFannotation.flanks.gff\n" ] } ], "source": [ "!head {paFlanks}\n", "!wc -l {paFlanks}" ] }, { "cell_type": "code", "execution_count": 158, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "scaffold6_cov64\tAUGUSTUS\tgene\t5653\t5804\t0.46\t-\t.\tg1\n", "scaffold6_cov64\tAUGUSTUS\tgene\t5653\t5804\t0.57\t+\t.\tg2\n", "scaffold7_cov100\tAUGUSTUS\tgene\t6218\t7068\t0.78\t-\t.\tg4\n", "scaffold7_cov100\tAUGUSTUS\tgene\t9074\t9589\t1\t-\t.\tg5\n", "scaffold7_cov100\tAUGUSTUS\tgene\t11671\t12670\t0.8\t-\t.\tg6\n", "scaffold7_cov100\tAUGUSTUS\tgene\t15464\t15737\t0.92\t-\t.\tg7\n", "scaffold7_cov100\tAUGUSTUS\tgene\t15464\t15737\t0.96\t+\t.\tg8\n", "scaffold7_cov100\tAUGUSTUS\tgene\t19271\t19311\t0.99\t-\t.\tg9\n", "scaffold7_cov100\tAUGUSTUS\tgene\t20051\t20077\t0.99\t-\t.\tg9\n", "scaffold7_cov100\tAUGUSTUS\tgene\t18321\t18585\t0.74\t+\t.\tg10\n", " 70639 ../../../genome-feature-files/Pact.GFFannotation.flanks.Upstream.gff\n" ] } ], "source": [ "!head {paUpstream}\n", "!wc -l {paUpstream}" ] }, { "cell_type": "code", "execution_count": 159, "metadata": { "collapsed": false, "scrolled": true }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "scaffold6_cov64\tAUGUSTUS\tgene\t1\t0\t0.46\t-\t.\tg1\n", "scaffold6_cov64\tAUGUSTUS\tgene\t6679\t7678\t0.57\t+\t.\tg2\n", "scaffold7_cov100\tAUGUSTUS\tgene\t2567\t3466\t0.96\t+\t.\tg3\n", "scaffold7_cov100\tAUGUSTUS\tgene\t2567\t3466\t0.78\t-\t.\tg4\n", "scaffold7_cov100\tAUGUSTUS\tgene\t6218\t7068\t1\t-\t.\tg5\n", "scaffold7_cov100\tAUGUSTUS\tgene\t9074\t9589\t0.8\t-\t.\tg6\n", "scaffold7_cov100\tAUGUSTUS\tgene\t12339\t13338\t0.92\t-\t.\tg7\n", "scaffold7_cov100\tAUGUSTUS\tgene\t18321\t18585\t0.96\t+\t.\tg8\n", "scaffold7_cov100\tAUGUSTUS\tgene\t19271\t19311\t0.96\t+\t.\tg8\n", "scaffold7_cov100\tAUGUSTUS\tgene\t18321\t18585\t0.99\t-\t.\tg9\n", " 73996 ../../../genome-feature-files/Pact.GFFannotation.flanks.Downstream.gff\n" ] } ], "source": [ "!head {paDownstream}\n", "!wc -l {paDownstream}" ] }, { "cell_type": "code", "execution_count": 160, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "scaffold1_cov55\t0\t421\n", "scaffold2_cov51\t0\t1151\n", "scaffold3_cov83\t0\t598\n", "scaffold4_cov57\t0\t192\n", "scaffold5_cov26\t0\t102\n", "scaffold6_cov64\t7678\t8236\n", "scaffold7_cov100\t25295\t27516\n", "scaffold7_cov100\t30779\t30897\n", "scaffold7_cov100\t38761\t40187\n", "scaffold7_cov100\t83819\t86977\n", " 185643 ../../../genome-feature-files/Pact.GFFannotation.intergenic.bed\n" ] } ], "source": [ "!head {paIntergenic}\n", "!wc -l {paIntergenic}" ] }, { "cell_type": "code", "execution_count": 161, "metadata": { "collapsed": false, "scrolled": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "##gff-version 2.0\n", "##date 2020-03-29\n", "##Type DNA scaffold1_cov55\n", "scaffold1_cov55\tfuzznuc\tmisc_feature\t23\t24\t2.000\t+\t.\tSequence \"scaffold1_cov55.1\" ; note \"*pat pattern1\"\n", "scaffold1_cov55\tfuzznuc\tmisc_feature\t35\t36\t2.000\t+\t.\tSequence \"scaffold1_cov55.2\" ; note \"*pat pattern1\"\n", "scaffold1_cov55\tfuzznuc\tmisc_feature\t50\t51\t2.000\t+\t.\tSequence \"scaffold1_cov55.3\" ; note \"*pat pattern1\"\n", "scaffold1_cov55\tfuzznuc\tmisc_feature\t85\t86\t2.000\t+\t.\tSequence \"scaffold1_cov55.4\" ; note \"*pat pattern1\"\n", "scaffold1_cov55\tfuzznuc\tmisc_feature\t93\t94\t2.000\t+\t.\tSequence \"scaffold1_cov55.5\" ; note \"*pat pattern1\"\n", "scaffold1_cov55\tfuzznuc\tmisc_feature\t103\t104\t2.000\t+\t.\tSequence \"scaffold1_cov55.6\" ; note \"*pat pattern1\"\n", "scaffold1_cov55\tfuzznuc\tmisc_feature\t106\t107\t2.000\t+\t.\tSequence \"scaffold1_cov55.7\" ; note \"*pat pattern1\"\n", " 9639415 ../../../genome-feature-files/Pact_CpG.gff\n" ] } ], "source": [ "!head {paCGMotifs}\n", "!wc -l {paCGMotifs}" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "#### 1c. Characterize overlaps with `bedtools`" ] }, { "cell_type": "code", "execution_count": 127, "metadata": { "collapsed": false }, "outputs": [], "source": [ "!{bedtoolsDirectory}intersectBed \\\n", "-u \\\n", "-a {paCGMotifs} \\\n", "-b {paGenes} \\\n", "> Pact-CGMotif-Gene-Overlaps.txt" ] }, { "cell_type": "code", "execution_count": 128, "metadata": { "collapsed": false }, "outputs": [], "source": [ "!{bedtoolsDirectory}intersectBed \\\n", "-u \\\n", "-a {paCGMotifs} \\\n", "-b {paCDS} \\\n", "> Pact-CGMotif-CDS-Overlaps.txt" ] }, { "cell_type": "code", "execution_count": 129, "metadata": { "collapsed": false }, "outputs": [], "source": [ "!{bedtoolsDirectory}intersectBed \\\n", "-u \\\n", "-a {paCGMotifs} \\\n", "-b {paIntron} \\\n", "> Pact-CGMotif-Intron-Overlaps.txt" ] }, { "cell_type": "code", "execution_count": 130, "metadata": { "collapsed": false }, "outputs": [], "source": [ "!{bedtoolsDirectory}intersectBed \\\n", "-u \\\n", "-a {paCGMotifs} \\\n", "-b {paFlanks} \\\n", "> Pact-CGMotif-Flanks-Overlaps.txt" ] }, { "cell_type": "code", "execution_count": 131, "metadata": { "collapsed": false }, "outputs": [], "source": [ "!{bedtoolsDirectory}intersectBed \\\n", "-u \\\n", "-a {paCGMotifs} \\\n", "-b {paUpstream} \\\n", "> Pact-CGMotif-Flanks-Upstream-Overlaps.txt" ] }, { "cell_type": "code", "execution_count": 132, "metadata": { "collapsed": false }, "outputs": [], "source": [ "!{bedtoolsDirectory}intersectBed \\\n", "-u \\\n", "-a {paCGMotifs} \\\n", "-b {paDownstream} \\\n", "> Pact-CGMotif-Flanks-Downstream-Overlaps.txt" ] }, { "cell_type": "code", "execution_count": 133, "metadata": { "collapsed": false }, "outputs": [], "source": [ "!{bedtoolsDirectory}intersectBed \\\n", "-u \\\n", "-a {paCGMotifs} \\\n", "-b {paIntergenic} \\\n", "> Pact-CGMotif-Intergenic-Overlaps.txt" ] }, { "cell_type": "code", "execution_count": 134, "metadata": { "collapsed": false }, "outputs": [], "source": [ "!wc -l *CGMotif* > Pact-CGMotif-Overlaps-counts.txt" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "#### 1d. Summary" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "| *P. acuta* Genome Feature \t| **Number individual features** \t| **Overlaps with CG Motifs** \t| **% Total CG Motifs** \t|\n", "|:-------------------------------:\t|:------------------------------:\t|:---------------------------:\t|:---------------------:\t|\n", "| Genes \t| 64558 \t| 3434720 \t| 35.6 \t|\n", "| Coding Sequences \t| 318484 \t| 1455630 \t| 15.1 \t|\n", "| Introns \t| 241534 \t| 1999490 \t| 20.7 \t|\n", "| Flanking Regions \t| 143874 \t| 1732726 \t| 17.8 \t|\n", "| Upstream Flanks \t| 70639 \t| 1047316 \t| 10.9 \t|\n", "| Downstream Flanks \t| 73996 \t| 948914 \t| 9.8 \t|\n", "| Intergenic Regions \t| 185643 \t| 3989278 \t| 41.4 \t|" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "### 2. Download coverage files" ] }, { "cell_type": "code", "execution_count": 162, "metadata": { "collapsed": false, "scrolled": true }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "--2020-07-09 11:01:09-- https://gannet.fish.washington.edu/seashell/bu-mox/scrubbed/031520-TG-bs/Pact_tg/dedup/\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", "HTTP request sent, awaiting response... 200 OK\n", "Length: unspecified [text/html]\n", "Saving to: ‘gannet.fish.washington.edu/seashell/bu-mox/scrubbed/031520-TG-bs/Pact_tg/dedup/index.html.tmp’\n", "\n", "gannet.fish.washing [ <=> ] 42.11K --.-KB/s in 0.001s \n", "\n", "2020-07-09 11:01:11 (34.9 MB/s) - ‘gannet.fish.washington.edu/seashell/bu-mox/scrubbed/031520-TG-bs/Pact_tg/dedup/index.html.tmp’ saved [43123]\n", "\n", "Loading robots.txt; please ignore errors.\n", "--2020-07-09 11:01:11-- 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", "2020-07-09 11:01:11 ERROR 404: Not Found.\n", "\n", "Removing gannet.fish.washington.edu/seashell/bu-mox/scrubbed/031520-TG-bs/Pact_tg/dedup/index.html.tmp since it should be rejected.\n", "\n", "--2020-07-09 11:01:11-- https://gannet.fish.washington.edu/seashell/bu-mox/scrubbed/031520-TG-bs/Pact_tg/dedup/?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: ‘gannet.fish.washington.edu/seashell/bu-mox/scrubbed/031520-TG-bs/Pact_tg/dedup/index.html?C=N;O=D.tmp’\n", "\n", "gannet.fish.washing [ <=> ] 42.11K --.-KB/s in 0.001s \n", "\n", "2020-07-09 11:01:12 (27.6 MB/s) - ‘gannet.fish.washington.edu/seashell/bu-mox/scrubbed/031520-TG-bs/Pact_tg/dedup/index.html?C=N;O=D.tmp’ saved [43123]\n", "\n", "Removing gannet.fish.washington.edu/seashell/bu-mox/scrubbed/031520-TG-bs/Pact_tg/dedup/index.html?C=N;O=D.tmp since it should be rejected.\n", "\n", "--2020-07-09 11:01:12-- https://gannet.fish.washington.edu/seashell/bu-mox/scrubbed/031520-TG-bs/Pact_tg/dedup/?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: ‘gannet.fish.washington.edu/seashell/bu-mox/scrubbed/031520-TG-bs/Pact_tg/dedup/index.html?C=M;O=A.tmp’\n", "\n", "gannet.fish.washing [ <=> ] 42.11K --.-KB/s in 0.002s \n", "\n", "2020-07-09 11:01:13 (25.6 MB/s) - ‘gannet.fish.washington.edu/seashell/bu-mox/scrubbed/031520-TG-bs/Pact_tg/dedup/index.html?C=M;O=A.tmp’ saved [43123]\n", "\n", "Removing gannet.fish.washington.edu/seashell/bu-mox/scrubbed/031520-TG-bs/Pact_tg/dedup/index.html?C=M;O=A.tmp since it should be rejected.\n", "\n", "--2020-07-09 11:01:13-- https://gannet.fish.washington.edu/seashell/bu-mox/scrubbed/031520-TG-bs/Pact_tg/dedup/?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: ‘gannet.fish.washington.edu/seashell/bu-mox/scrubbed/031520-TG-bs/Pact_tg/dedup/index.html?C=S;O=A.tmp’\n", "\n", "gannet.fish.washing [ <=> ] 42.11K --.-KB/s in 0.001s \n", "\n", "2020-07-09 11:01:14 (32.6 MB/s) - ‘gannet.fish.washington.edu/seashell/bu-mox/scrubbed/031520-TG-bs/Pact_tg/dedup/index.html?C=S;O=A.tmp’ saved [43123]\n", "\n", "Removing gannet.fish.washington.edu/seashell/bu-mox/scrubbed/031520-TG-bs/Pact_tg/dedup/index.html?C=S;O=A.tmp since it should be rejected.\n", "\n", "--2020-07-09 11:01:14-- https://gannet.fish.washington.edu/seashell/bu-mox/scrubbed/031520-TG-bs/Pact_tg/dedup/?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: ‘gannet.fish.washington.edu/seashell/bu-mox/scrubbed/031520-TG-bs/Pact_tg/dedup/index.html?C=D;O=A.tmp’\n", "\n", "gannet.fish.washing [ <=> ] 42.11K --.-KB/s in 0.004s \n", "\n", "2020-07-09 11:01:15 (10.7 MB/s) - ‘gannet.fish.washington.edu/seashell/bu-mox/scrubbed/031520-TG-bs/Pact_tg/dedup/index.html?C=D;O=A.tmp’ saved [43123]\n", "\n", "Removing gannet.fish.washington.edu/seashell/bu-mox/scrubbed/031520-TG-bs/Pact_tg/dedup/index.html?C=D;O=A.tmp since it should be rejected.\n", "\n", "--2020-07-09 11:01:15-- https://gannet.fish.washington.edu/seashell/bu-mox/scrubbed/031520-TG-bs/Pact_tg/dedup/Meth1_R1_001_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: 226808063 (216M)\n", "Saving to: ‘gannet.fish.washington.edu/seashell/bu-mox/scrubbed/031520-TG-bs/Pact_tg/dedup/Meth1_R1_001_val_1_bismark_bt2_pe._5x.bedgraph’\n", "\n", "gannet.fish.washing 100%[===================>] 216.30M 80.9MB/s in 2.7s \n", "\n", "2020-07-09 11:01:18 (80.9 MB/s) - ‘gannet.fish.washington.edu/seashell/bu-mox/scrubbed/031520-TG-bs/Pact_tg/dedup/Meth1_R1_001_val_1_bismark_bt2_pe._5x.bedgraph’ saved [226808063/226808063]\n", "\n", "--2020-07-09 11:01:18-- https://gannet.fish.washington.edu/seashell/bu-mox/scrubbed/031520-TG-bs/Pact_tg/dedup/Meth2_R1_001_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: 259720833 (248M)\n", "Saving to: ‘gannet.fish.washington.edu/seashell/bu-mox/scrubbed/031520-TG-bs/Pact_tg/dedup/Meth2_R1_001_val_1_bismark_bt2_pe._5x.bedgraph’\n", "\n", "gannet.fish.washing 100%[===================>] 247.69M 81.3MB/s in 3.0s \n", "\n", "2020-07-09 11:01:21 (81.3 MB/s) - ‘gannet.fish.washington.edu/seashell/bu-mox/scrubbed/031520-TG-bs/Pact_tg/dedup/Meth2_R1_001_val_1_bismark_bt2_pe._5x.bedgraph’ saved [259720833/259720833]\n", "\n", "--2020-07-09 11:01:21-- https://gannet.fish.washington.edu/seashell/bu-mox/scrubbed/031520-TG-bs/Pact_tg/dedup/Meth3_R1_001_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: 239858422 (229M)\n", "Saving to: ‘gannet.fish.washington.edu/seashell/bu-mox/scrubbed/031520-TG-bs/Pact_tg/dedup/Meth3_R1_001_val_1_bismark_bt2_pe._5x.bedgraph’\n", "\n", "gannet.fish.washing 100%[===================>] 228.75M 87.1MB/s in 2.6s \n", "\n", "2020-07-09 11:01:24 (87.1 MB/s) - ‘gannet.fish.washington.edu/seashell/bu-mox/scrubbed/031520-TG-bs/Pact_tg/dedup/Meth3_R1_001_val_1_bismark_bt2_pe._5x.bedgraph’ saved [239858422/239858422]\n", "\n", "--2020-07-09 11:01:24-- https://gannet.fish.washington.edu/seashell/bu-mox/scrubbed/031520-TG-bs/Pact_tg/dedup/Meth7_R1_001_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: 107859832 (103M)\n", "Saving to: ‘gannet.fish.washington.edu/seashell/bu-mox/scrubbed/031520-TG-bs/Pact_tg/dedup/Meth7_R1_001_val_1_bismark_bt2_pe._5x.bedgraph’\n", "\n", "gannet.fish.washing 100%[===================>] 102.86M 72.8MB/s in 1.4s \n", "\n", "2020-07-09 11:01:25 (72.8 MB/s) - ‘gannet.fish.washington.edu/seashell/bu-mox/scrubbed/031520-TG-bs/Pact_tg/dedup/Meth7_R1_001_val_1_bismark_bt2_pe._5x.bedgraph’ saved [107859832/107859832]\n", "\n", "--2020-07-09 11:01:25-- https://gannet.fish.washington.edu/seashell/bu-mox/scrubbed/031520-TG-bs/Pact_tg/dedup/Meth8_R1_001_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: 21772891 (21M)\n", "Saving to: ‘gannet.fish.washington.edu/seashell/bu-mox/scrubbed/031520-TG-bs/Pact_tg/dedup/Meth8_R1_001_val_1_bismark_bt2_pe._5x.bedgraph’\n", "\n", "gannet.fish.washing 100%[===================>] 20.76M 93.6MB/s in 0.2s \n", "\n", "2020-07-09 11:01:26 (93.6 MB/s) - ‘gannet.fish.washington.edu/seashell/bu-mox/scrubbed/031520-TG-bs/Pact_tg/dedup/Meth8_R1_001_val_1_bismark_bt2_pe._5x.bedgraph’ saved [21772891/21772891]\n", "\n", "--2020-07-09 11:01:26-- https://gannet.fish.washington.edu/seashell/bu-mox/scrubbed/031520-TG-bs/Pact_tg/dedup/Meth9_R1_001_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: 111717514 (107M)\n", "Saving to: ‘gannet.fish.washington.edu/seashell/bu-mox/scrubbed/031520-TG-bs/Pact_tg/dedup/Meth9_R1_001_val_1_bismark_bt2_pe._5x.bedgraph’\n", "\n", "gannet.fish.washing 100%[===================>] 106.54M 55.7MB/s in 1.9s \n", "\n", "2020-07-09 11:01:28 (55.7 MB/s) - ‘gannet.fish.washington.edu/seashell/bu-mox/scrubbed/031520-TG-bs/Pact_tg/dedup/Meth9_R1_001_val_1_bismark_bt2_pe._5x.bedgraph’ saved [111717514/111717514]\n", "\n", "FINISHED --2020-07-09 11:01:28--\n", "Total wall clock time: 18s\n", "Downloaded: 11 files, 923M in 12s (77.5 MB/s)\n" ] } ], "source": [ "#Download Pact WGBS and MBD-BS 5x sample bedgraphs\n", "!wget -r -l1 --no-parent -A \"*5x.bedgraph\" https://gannet.fish.washington.edu/seashell/bu-mox/scrubbed/031520-TG-bs/Pact_tg/dedup/" ] }, { "cell_type": "code", "execution_count": 163, "metadata": { "collapsed": true }, "outputs": [], "source": [ "#Move samples from directory structure on gannet to cd\n", "!mv gannet.fish.washington.edu/seashell/bu-mox/scrubbed/031520-TG-bs/Pact_tg/dedup/* ." ] }, { "cell_type": "code", "execution_count": 164, "metadata": { "collapsed": true }, "outputs": [], "source": [ "#Remove empty directory\n", "!rm -r gannet.fish.washington.edu/" ] }, { "cell_type": "code", "execution_count": 165, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "Meth1_R1_001_val_1_bismark_bt2_pe._5x.bedgraph\r\n", "Meth2_R1_001_val_1_bismark_bt2_pe._5x.bedgraph\r\n", "Meth3_R1_001_val_1_bismark_bt2_pe._5x.bedgraph\r\n", "Meth7_R1_001_val_1_bismark_bt2_pe._5x.bedgraph\r\n", "Meth8_R1_001_val_1_bismark_bt2_pe._5x.bedgraph\r\n", "Meth9_R1_001_val_1_bismark_bt2_pe._5x.bedgraph\r\n" ] } ], "source": [ "#Check files\n", "!find *bedgraph" ] }, { "cell_type": "code", "execution_count": 166, "metadata": { "collapsed": false, "scrolled": true }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "--2020-07-09 11:01:28-- https://gannet.fish.washington.edu/seashell/bu-mox/scrubbed/031520-TG-bs/Pact_tg/nodedup/\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", "HTTP request sent, awaiting response... 200 OK\n", "Length: unspecified [text/html]\n", "Saving to: ‘gannet.fish.washington.edu/seashell/bu-mox/scrubbed/031520-TG-bs/Pact_tg/nodedup/index.html.tmp’\n", "\n", "gannet.fish.washing [ <=> ] 19.51K --.-KB/s in 0.001s \n", "\n", "2020-07-09 11:01:29 (37.8 MB/s) - ‘gannet.fish.washington.edu/seashell/bu-mox/scrubbed/031520-TG-bs/Pact_tg/nodedup/index.html.tmp’ saved [19983]\n", "\n", "Loading robots.txt; please ignore errors.\n", "--2020-07-09 11:01:29-- 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", "2020-07-09 11:01:29 ERROR 404: Not Found.\n", "\n", "Removing gannet.fish.washington.edu/seashell/bu-mox/scrubbed/031520-TG-bs/Pact_tg/nodedup/index.html.tmp since it should be rejected.\n", "\n", "--2020-07-09 11:01:29-- https://gannet.fish.washington.edu/seashell/bu-mox/scrubbed/031520-TG-bs/Pact_tg/nodedup/?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: ‘gannet.fish.washington.edu/seashell/bu-mox/scrubbed/031520-TG-bs/Pact_tg/nodedup/index.html?C=N;O=D.tmp’\n", "\n", "gannet.fish.washing [ <=> ] 19.51K --.-KB/s in 0.001s \n", "\n", "2020-07-09 11:01:30 (26.2 MB/s) - ‘gannet.fish.washington.edu/seashell/bu-mox/scrubbed/031520-TG-bs/Pact_tg/nodedup/index.html?C=N;O=D.tmp’ saved [19983]\n", "\n", "Removing gannet.fish.washington.edu/seashell/bu-mox/scrubbed/031520-TG-bs/Pact_tg/nodedup/index.html?C=N;O=D.tmp since it should be rejected.\n", "\n", "--2020-07-09 11:01:30-- https://gannet.fish.washington.edu/seashell/bu-mox/scrubbed/031520-TG-bs/Pact_tg/nodedup/?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: ‘gannet.fish.washington.edu/seashell/bu-mox/scrubbed/031520-TG-bs/Pact_tg/nodedup/index.html?C=M;O=A.tmp’\n", "\n", "gannet.fish.washing [ <=> ] 19.51K --.-KB/s in 0.001s \n", "\n", "2020-07-09 11:01:30 (29.4 MB/s) - ‘gannet.fish.washington.edu/seashell/bu-mox/scrubbed/031520-TG-bs/Pact_tg/nodedup/index.html?C=M;O=A.tmp’ saved [19983]\n", "\n", "Removing gannet.fish.washington.edu/seashell/bu-mox/scrubbed/031520-TG-bs/Pact_tg/nodedup/index.html?C=M;O=A.tmp since it should be rejected.\n", "\n", "--2020-07-09 11:01:30-- https://gannet.fish.washington.edu/seashell/bu-mox/scrubbed/031520-TG-bs/Pact_tg/nodedup/?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: ‘gannet.fish.washington.edu/seashell/bu-mox/scrubbed/031520-TG-bs/Pact_tg/nodedup/index.html?C=S;O=A.tmp’\n", "\n", "gannet.fish.washing [ <=> ] 19.51K --.-KB/s in 0s \n", "\n", "2020-07-09 11:01:30 (55.6 MB/s) - ‘gannet.fish.washington.edu/seashell/bu-mox/scrubbed/031520-TG-bs/Pact_tg/nodedup/index.html?C=S;O=A.tmp’ saved [19983]\n", "\n", "Removing gannet.fish.washington.edu/seashell/bu-mox/scrubbed/031520-TG-bs/Pact_tg/nodedup/index.html?C=S;O=A.tmp since it should be rejected.\n", "\n", "--2020-07-09 11:01:30-- https://gannet.fish.washington.edu/seashell/bu-mox/scrubbed/031520-TG-bs/Pact_tg/nodedup/?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: ‘gannet.fish.washington.edu/seashell/bu-mox/scrubbed/031520-TG-bs/Pact_tg/nodedup/index.html?C=D;O=A.tmp’\n", "\n", "gannet.fish.washing [ <=> ] 19.51K --.-KB/s in 0.001s \n", "\n", "2020-07-09 11:01:31 (27.9 MB/s) - ‘gannet.fish.washington.edu/seashell/bu-mox/scrubbed/031520-TG-bs/Pact_tg/nodedup/index.html?C=D;O=A.tmp’ saved [19983]\n", "\n", "Removing gannet.fish.washington.edu/seashell/bu-mox/scrubbed/031520-TG-bs/Pact_tg/nodedup/index.html?C=D;O=A.tmp since it should be rejected.\n", "\n", "--2020-07-09 11:01:31-- https://gannet.fish.washington.edu/seashell/bu-mox/scrubbed/031520-TG-bs/Pact_tg/nodedup/Meth4_R1_001_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: 74748447 (71M)\n", "Saving to: ‘gannet.fish.washington.edu/seashell/bu-mox/scrubbed/031520-TG-bs/Pact_tg/nodedup/Meth4_R1_001_val_1_bismark_bt2_pe._5x.bedgraph’\n", "\n", "gannet.fish.washing 100%[===================>] 71.29M 79.8MB/s in 0.9s \n", "\n", "2020-07-09 11:01:32 (79.8 MB/s) - ‘gannet.fish.washington.edu/seashell/bu-mox/scrubbed/031520-TG-bs/Pact_tg/nodedup/Meth4_R1_001_val_1_bismark_bt2_pe._5x.bedgraph’ saved [74748447/74748447]\n", "\n", "--2020-07-09 11:01:32-- https://gannet.fish.washington.edu/seashell/bu-mox/scrubbed/031520-TG-bs/Pact_tg/nodedup/Meth5_R1_001_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: 58979704 (56M)\n", "Saving to: ‘gannet.fish.washington.edu/seashell/bu-mox/scrubbed/031520-TG-bs/Pact_tg/nodedup/Meth5_R1_001_val_1_bismark_bt2_pe._5x.bedgraph’\n", "\n", "gannet.fish.washing 100%[===================>] 56.25M 92.6MB/s in 0.6s \n", "\n", "2020-07-09 11:01:32 (92.6 MB/s) - ‘gannet.fish.washington.edu/seashell/bu-mox/scrubbed/031520-TG-bs/Pact_tg/nodedup/Meth5_R1_001_val_1_bismark_bt2_pe._5x.bedgraph’ saved [58979704/58979704]\n", "\n", "--2020-07-09 11:01:32-- https://gannet.fish.washington.edu/seashell/bu-mox/scrubbed/031520-TG-bs/Pact_tg/nodedup/Meth6_R1_001_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: 61726619 (59M)\n", "Saving to: ‘gannet.fish.washington.edu/seashell/bu-mox/scrubbed/031520-TG-bs/Pact_tg/nodedup/Meth6_R1_001_val_1_bismark_bt2_pe._5x.bedgraph’\n", "\n", "gannet.fish.washing 100%[===================>] 58.87M 94.5MB/s in 0.6s \n", "\n", "2020-07-09 11:01:33 (94.5 MB/s) - ‘gannet.fish.washington.edu/seashell/bu-mox/scrubbed/031520-TG-bs/Pact_tg/nodedup/Meth6_R1_001_val_1_bismark_bt2_pe._5x.bedgraph’ saved [61726619/61726619]\n", "\n", "FINISHED --2020-07-09 11:01:33--\n", "Total wall clock time: 4.8s\n", "Downloaded: 8 files, 186M in 2.1s (87.7 MB/s)\n" ] } ], "source": [ "#Download Pact RRBS 5x sample bedgraphs\n", "!wget -r -l1 --no-parent -A \"*5x.bedgraph\" https://gannet.fish.washington.edu/seashell/bu-mox/scrubbed/031520-TG-bs/Pact_tg/nodedup/" ] }, { "cell_type": "code", "execution_count": 167, "metadata": { "collapsed": true }, "outputs": [], "source": [ "#Move samples from directory structure on gannet to cd\n", "!mv gannet.fish.washington.edu/seashell/bu-mox/scrubbed/031520-TG-bs/Pact_tg/nodedup/* ." ] }, { "cell_type": "code", "execution_count": 168, "metadata": { "collapsed": true }, "outputs": [], "source": [ "#Remove empty directory\n", "!rm -r gannet.fish.washington.edu/" ] }, { "cell_type": "code", "execution_count": 169, "metadata": { "collapsed": false, "scrolled": true }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "Meth1_R1_001_val_1_bismark_bt2_pe._5x.bedgraph\r\n", "Meth2_R1_001_val_1_bismark_bt2_pe._5x.bedgraph\r\n", "Meth3_R1_001_val_1_bismark_bt2_pe._5x.bedgraph\r\n", "Meth4_R1_001_val_1_bismark_bt2_pe._5x.bedgraph\r\n", "Meth5_R1_001_val_1_bismark_bt2_pe._5x.bedgraph\r\n", "Meth6_R1_001_val_1_bismark_bt2_pe._5x.bedgraph\r\n", "Meth7_R1_001_val_1_bismark_bt2_pe._5x.bedgraph\r\n", "Meth8_R1_001_val_1_bismark_bt2_pe._5x.bedgraph\r\n", "Meth9_R1_001_val_1_bismark_bt2_pe._5x.bedgraph\r\n" ] } ], "source": [ "!find *bedgraph" ] }, { "cell_type": "code", "execution_count": 170, "metadata": { "collapsed": false, "scrolled": true }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "Meth8_R1_001_val_1_bismark_bt2_pe._5x.bedgraph: OK\n", "Meth9_R1_001_val_1_bismark_bt2_pe._5x.bedgraph: OK\n", "Meth2_R1_001_val_1_bismark_bt2_pe._5x.bedgraph: OK\n", "Meth3_R1_001_val_1_bismark_bt2_pe._5x.bedgraph: OK\n", "Meth1_R1_001_val_1_bismark_bt2_pe._5x.bedgraph: OK\n", "Meth7_R1_001_val_1_bismark_bt2_pe._5x.bedgraph: OK\n", "Meth6_R1_001_val_1_bismark_bt2_pe._5x.bedgraph: OK\n", "Meth5_R1_001_val_1_bismark_bt2_pe._5x.bedgraph: OK\n", "Meth4_R1_001_val_1_bismark_bt2_pe._5x.bedgraph: OK\n" ] } ], "source": [ "#Verify checksums from gannet\n", "!md5sum -c ../Pact-5xbedgraph-GANNET-md5sum.txt" ] }, { "cell_type": "code", "execution_count": 171, "metadata": { "collapsed": false, "scrolled": true }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ " 5546051 Meth1_R1_001_val_1_bismark_bt2_pe._5x.bedgraph\n", " 6358722 Meth2_R1_001_val_1_bismark_bt2_pe._5x.bedgraph\n", " 5866786 Meth3_R1_001_val_1_bismark_bt2_pe._5x.bedgraph\n", " 1835561 Meth4_R1_001_val_1_bismark_bt2_pe._5x.bedgraph\n", " 1451229 Meth5_R1_001_val_1_bismark_bt2_pe._5x.bedgraph\n", " 1517358 Meth6_R1_001_val_1_bismark_bt2_pe._5x.bedgraph\n", " 2640625 Meth7_R1_001_val_1_bismark_bt2_pe._5x.bedgraph\n", " 539008 Meth8_R1_001_val_1_bismark_bt2_pe._5x.bedgraph\n", " 2732607 Meth9_R1_001_val_1_bismark_bt2_pe._5x.bedgraph\n", " 28487947 total\n" ] } ], "source": [ "!wc -l *bedgraph" ] }, { "cell_type": "code", "execution_count": 172, "metadata": { "collapsed": true }, "outputs": [], "source": [ "!wc -l *bedgraph > Pact-5x-bedgraph-counts.txt" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "### 3. Characterize methylation for each CpG dinucleotide\n", "\n", "- Methylated: > 50% methylation\n", "- Sparsely methylated: 10-50% methylation\n", "- Unmethylated: < 10% methylation" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "##### Methylated loci" ] }, { "cell_type": "code", "execution_count": 173, "metadata": { "collapsed": true }, "outputs": [], "source": [ "%%bash\n", "for f in *bedgraph\n", "do\n", " awk '{if ($4 >= 50) { print $1, $2, $3, $4 }}' ${f} \\\n", " > ${f}-Meth\n", "done" ] }, { "cell_type": "code", "execution_count": 174, "metadata": { "collapsed": false, "scrolled": true }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "==> Meth1_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth <==\n", "scaffold7_cov100 4351 4353 50.000000\n", "scaffold7_cov100 5500 5502 83.333333\n", "scaffold7_cov100 5578 5580 57.142857\n", "scaffold7_cov100 5986 5988 100.000000\n", "scaffold7_cov100 6144 6146 100.000000\n", "scaffold7_cov100 6188 6190 100.000000\n", "scaffold7_cov100 6198 6200 88.888889\n", "scaffold7_cov100 6231 6233 100.000000\n", "scaffold7_cov100 6233 6235 100.000000\n", "scaffold7_cov100 7438 7440 100.000000\n", "\n", "==> Meth2_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth <==\n", "scaffold7_cov100 5500 5502 62.500000\n", "scaffold7_cov100 5986 5988 66.666667\n", "scaffold7_cov100 6144 6146 100.000000\n", "scaffold7_cov100 6188 6190 94.117647\n", "scaffold7_cov100 6198 6200 100.000000\n", "scaffold7_cov100 6231 6233 71.428571\n", "scaffold7_cov100 6233 6235 100.000000\n", "scaffold7_cov100 7438 7440 88.235294\n", "scaffold7_cov100 7696 7698 95.833333\n", "scaffold7_cov100 7796 7798 60.000000\n", "\n", "==> Meth3_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth <==\n", "scaffold7_cov100 5500 5502 87.500000\n", "scaffold7_cov100 5578 5580 55.555556\n", "scaffold7_cov100 5986 5988 60.000000\n", "scaffold7_cov100 6144 6146 100.000000\n", "scaffold7_cov100 6188 6190 100.000000\n", "scaffold7_cov100 6198 6200 100.000000\n", "scaffold7_cov100 6231 6233 100.000000\n", "scaffold7_cov100 6233 6235 100.000000\n", "scaffold7_cov100 7438 7440 100.000000\n", "scaffold7_cov100 7696 7698 100.000000\n", "\n", "==> Meth4_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth <==\n", "scaffold7_cov100 1535 1537 60.000000\n", "scaffold7_cov100 24509 24511 100.000000\n", "scaffold7_cov100 24557 24559 100.000000\n", "scaffold7_cov100 33140 33142 80.000000\n", "scaffold7_cov100 33157 33159 80.000000\n", "scaffold7_cov100 40896 40898 50.000000\n", "scaffold7_cov100 84631 84633 62.500000\n", "scaffold7_cov100 96791 96793 65.000000\n", "scaffold7_cov100 109716 109718 60.000000\n", "scaffold7_cov100 138357 138359 100.000000\n", "\n", "==> Meth5_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth <==\n", "scaffold6_cov64 2676 2678 77.777778\n", "scaffold7_cov100 2301 2303 50.000000\n", "scaffold7_cov100 17000 17002 100.000000\n", "scaffold7_cov100 17090 17092 100.000000\n", "scaffold7_cov100 24454 24456 100.000000\n", "scaffold7_cov100 24494 24496 87.500000\n", "scaffold7_cov100 24509 24511 100.000000\n", "scaffold7_cov100 24557 24559 100.000000\n", "scaffold7_cov100 61080 61082 57.142857\n", "scaffold7_cov100 69126 69128 80.000000\n", "\n", "==> Meth6_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth <==\n", "scaffold7_cov100 106242 106244 66.666667\n", "scaffold7_cov100 106251 106253 66.666667\n", "scaffold7_cov100 106254 106256 66.666667\n", "scaffold7_cov100 138357 138359 50.000000\n", "scaffold7_cov100 138372 138374 100.000000\n", "scaffold7_cov100 138390 138392 100.000000\n", "scaffold7_cov100 151631 151633 60.000000\n", "scaffold7_cov100 210167 210169 83.333333\n", "scaffold7_cov100 223257 223259 57.142857\n", "scaffold7_cov100 223265 223267 57.142857\n", "\n", "==> Meth7_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth <==\n", "scaffold3_cov83 118 120 60.000000\n", "scaffold3_cov83 137 139 50.000000\n", "scaffold3_cov83 261 263 69.444444\n", "scaffold3_cov83 475 477 72.727273\n", "scaffold3_cov83 484 486 64.705882\n", "scaffold3_cov83 504 506 83.333333\n", "scaffold7_cov100 5500 5502 70.000000\n", "scaffold7_cov100 5986 5988 73.333333\n", "scaffold7_cov100 6144 6146 96.666667\n", "scaffold7_cov100 6188 6190 93.181818\n", "\n", "==> Meth8_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth <==\n", "scaffold3_cov83 208 210 60.000000\n", "scaffold3_cov83 261 263 50.000000\n", "scaffold3_cov83 475 477 63.636364\n", "scaffold7_cov100 5986 5988 78.947368\n", "scaffold7_cov100 6144 6146 95.918367\n", "scaffold7_cov100 6188 6190 100.000000\n", "scaffold7_cov100 6198 6200 97.297297\n", "scaffold7_cov100 6233 6235 93.103448\n", "scaffold7_cov100 7696 7698 100.000000\n", "scaffold7_cov100 7796 7798 72.727273\n", "\n", "==> Meth9_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth <==\n", "scaffold7_cov100 5578 5580 66.666667\n", "scaffold7_cov100 5986 5988 79.166667\n", "scaffold7_cov100 6144 6146 96.296296\n", "scaffold7_cov100 6188 6190 92.592593\n", "scaffold7_cov100 6198 6200 94.339623\n", "scaffold7_cov100 6231 6233 95.555556\n", "scaffold7_cov100 6233 6235 97.619048\n", "scaffold7_cov100 7201 7203 80.000000\n", "scaffold7_cov100 7438 7440 100.000000\n", "scaffold7_cov100 7696 7698 91.304348\n" ] } ], "source": [ "!head *Meth" ] }, { "cell_type": "code", "execution_count": 175, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ " 110364 Meth1_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth\n", " 126440 Meth2_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth\n", " 124819 Meth3_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth\n", " 31047 Meth4_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth\n", " 30345 Meth5_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth\n", " 26617 Meth6_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth\n", " 258222 Meth7_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth\n", " 213342 Meth8_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth\n", " 255370 Meth9_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth\n", " 1176566 total\n" ] } ], "source": [ "!wc -l *Meth" ] }, { "cell_type": "code", "execution_count": 176, "metadata": { "collapsed": true }, "outputs": [], "source": [ "!wc -l *-Meth > Pact-5x-Meth-counts.txt" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "##### Sparsely methylated loci" ] }, { "cell_type": "code", "execution_count": 177, "metadata": { "collapsed": true }, "outputs": [], "source": [ "%%bash\n", "for f in *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": 178, "metadata": { "collapsed": false, "scrolled": true }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "==> Meth1_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth <==\r\n", "scaffold1_cov55 102 104 16.666667\r\n", "scaffold1_cov55 186 188 20.000000\r\n", "scaffold3_cov83 118 120 12.500000\r\n", "scaffold3_cov83 137 139 12.500000\r\n", "scaffold3_cov83 475 477 18.750000\r\n", "scaffold3_cov83 484 486 14.893617\r\n", "scaffold3_cov83 504 506 21.052632\r\n", "scaffold6_cov64 7373 7375 12.500000\r\n", "scaffold6_cov64 7983 7985 11.111111\r\n", "scaffold7_cov100 1293 1295 11.111111\r\n", "\r\n", "==> Meth2_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth <==\r\n", "scaffold1_cov55 105 107 12.500000\r\n", "scaffold1_cov55 252 254 20.000000\r\n", "scaffold2_cov51 686 688 11.111111\r\n", "scaffold6_cov64 3978 3980 11.111111\r\n", "scaffold6_cov64 7077 7079 12.500000\r\n", "scaffold7_cov100 2652 2654 16.666667\r\n", "scaffold7_cov100 3994 3996 10.526316\r\n", "scaffold7_cov100 7121 7123 25.000000\r\n", "scaffold7_cov100 7201 7203 16.666667\r\n", "scaffold7_cov100 10755 10757 13.333333\r\n", "\r\n", "==> Meth3_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth <==\r\n", "scaffold1_cov55 119 121 20.000000\r\n", "scaffold1_cov55 194 196 20.000000\r\n", "scaffold2_cov51 686 688 15.384615\r\n", "scaffold3_cov83 189 191 14.285714\r\n", "scaffold3_cov83 475 477 13.333333\r\n", "scaffold6_cov64 1725 1727 11.111111\r\n", "scaffold6_cov64 3533 3535 14.285714\r\n", "scaffold6_cov64 5904 5906 12.500000\r\n", "scaffold6_cov64 5992 5994 12.500000\r\n", "scaffold6_cov64 6732 6734 14.285714\r\n", "\r\n", "==> Meth4_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth <==\r\n", "scaffold6_cov64 2676 2678 20.000000\r\n", "scaffold6_cov64 5904 5906 15.485564\r\n", "scaffold6_cov64 6732 6734 16.666667\r\n", "scaffold7_cov100 1618 1620 12.500000\r\n", "scaffold7_cov100 1628 1630 14.285714\r\n", "scaffold7_cov100 4351 4353 46.428571\r\n", "scaffold7_cov100 15408 15410 20.000000\r\n", "scaffold7_cov100 38369 38371 11.111111\r\n", "scaffold7_cov100 39365 39367 25.000000\r\n", "scaffold7_cov100 39367 39369 25.000000\r\n", "\r\n", "==> Meth5_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth <==\r\n", "scaffold6_cov64 4553 4555 20.000000\r\n", "scaffold6_cov64 5545 5547 14.285714\r\n", "scaffold6_cov64 6374 6376 45.454545\r\n", "scaffold7_cov100 17074 17076 33.333333\r\n", "scaffold7_cov100 17098 17100 20.000000\r\n", "scaffold7_cov100 24443 24445 16.666667\r\n", "scaffold7_cov100 36543 36545 25.000000\r\n", "scaffold7_cov100 36600 36602 25.000000\r\n", "scaffold7_cov100 46343 46345 46.153846\r\n", "scaffold7_cov100 46428 46430 14.285714\r\n", "\r\n", "==> Meth6_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth <==\r\n", "scaffold6_cov64 4553 4555 14.285714\r\n", "scaffold6_cov64 4588 4590 22.222222\r\n", "scaffold6_cov64 5604 5606 11.538462\r\n", "scaffold6_cov64 6266 6268 14.285714\r\n", "scaffold6_cov64 6374 6376 20.000000\r\n", "scaffold6_cov64 6687 6689 14.285714\r\n", "scaffold6_cov64 6704 6706 14.285714\r\n", "scaffold6_cov64 7373 7375 16.666667\r\n", "scaffold7_cov100 4351 4353 10.256410\r\n", "scaffold7_cov100 28086 28088 16.666667\r\n", "\r\n", "==> Meth7_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth <==\r\n", "scaffold3_cov83 130 132 40.000000\r\n", "scaffold3_cov83 189 191 44.444444\r\n", "scaffold3_cov83 208 210 42.857143\r\n", "scaffold6_cov64 4146 4148 20.000000\r\n", "scaffold6_cov64 5561 5563 14.285714\r\n", "scaffold6_cov64 5644 5646 11.111111\r\n", "scaffold6_cov64 6805 6807 14.285714\r\n", "scaffold6_cov64 6880 6882 14.285714\r\n", "scaffold6_cov64 7609 7611 14.285714\r\n", "scaffold7_cov100 1422 1424 33.333333\r\n", "\r\n", "==> Meth8_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth <==\r\n", "scaffold3_cov83 484 486 45.454545\r\n", "scaffold3_cov83 504 506 20.000000\r\n", "scaffold6_cov64 826 828 14.285714\r\n", "scaffold7_cov100 5500 5502 11.764706\r\n", "scaffold7_cov100 6231 6233 42.857143\r\n", "scaffold7_cov100 7438 7440 40.000000\r\n", "scaffold7_cov100 12131 12133 40.000000\r\n", "scaffold7_cov100 12247 12249 37.500000\r\n", "scaffold7_cov100 12861 12863 27.272727\r\n", "scaffold7_cov100 13385 13387 46.666667\r\n", "\r\n", "==> Meth9_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth <==\r\n", "scaffold3_cov83 118 120 14.285714\r\n", "scaffold3_cov83 130 132 12.500000\r\n", "scaffold3_cov83 137 139 25.000000\r\n", "scaffold3_cov83 189 191 38.461538\r\n", "scaffold3_cov83 208 210 23.529412\r\n", "scaffold3_cov83 261 263 23.809524\r\n", "scaffold3_cov83 475 477 48.000000\r\n", "scaffold3_cov83 484 486 32.000000\r\n", "scaffold6_cov64 3435 3437 15.384615\r\n", "scaffold6_cov64 4146 4148 12.500000\r\n" ] } ], "source": [ "!head *sparseMeth" ] }, { "cell_type": "code", "execution_count": 179, "metadata": { "collapsed": false, "scrolled": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ " 367019 Meth1_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth\n", " 345887 Meth2_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth\n", " 385346 Meth3_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth\n", " 137700 Meth4_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth\n", " 64837 Meth5_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth\n", " 89246 Meth6_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth\n", " 296059 Meth7_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth\n", " 80086 Meth8_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth\n", " 337855 Meth9_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth\n", " 2104035 total\n" ] } ], "source": [ "!wc -l *sparseMeth" ] }, { "cell_type": "code", "execution_count": 180, "metadata": { "collapsed": true }, "outputs": [], "source": [ "!wc -l *-sparseMeth > Pact-5x-sparseMeth-counts.txt" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "##### Unmethylated loci" ] }, { "cell_type": "code", "execution_count": 181, "metadata": { "collapsed": true }, "outputs": [], "source": [ "%%bash\n", "for f in *bedgraph\n", "do\n", " awk '{if ($4 <= 10) { print $1, $2, $3, $4 }}' ${f} \\\n", " > ${f}-unMeth\n", "done" ] }, { "cell_type": "code", "execution_count": 182, "metadata": { "collapsed": false, "scrolled": true }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "==> Meth1_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth <==\n", "scaffold1_cov55 105 107 0.000000\n", "scaffold1_cov55 116 118 0.000000\n", "scaffold1_cov55 119 121 0.000000\n", "scaffold1_cov55 146 148 0.000000\n", "scaffold1_cov55 194 196 0.000000\n", "scaffold2_cov51 649 651 0.000000\n", "scaffold2_cov51 686 688 8.333333\n", "scaffold2_cov51 778 780 0.000000\n", "scaffold3_cov83 130 132 0.000000\n", "scaffold3_cov83 189 191 6.250000\n", "\n", "==> Meth2_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth <==\n", "scaffold1_cov55 49 51 0.000000\n", "scaffold1_cov55 84 86 0.000000\n", "scaffold1_cov55 92 94 0.000000\n", "scaffold1_cov55 102 104 0.000000\n", "scaffold1_cov55 116 118 0.000000\n", "scaffold1_cov55 119 121 0.000000\n", "scaffold1_cov55 146 148 0.000000\n", "scaffold1_cov55 169 171 0.000000\n", "scaffold1_cov55 186 188 0.000000\n", "scaffold1_cov55 194 196 0.000000\n", "\n", "==> Meth3_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth <==\n", "scaffold1_cov55 250 252 0.000000\n", "scaffold2_cov51 649 651 0.000000\n", "scaffold2_cov51 778 780 0.000000\n", "scaffold3_cov83 118 120 0.000000\n", "scaffold3_cov83 130 132 0.000000\n", "scaffold3_cov83 137 139 0.000000\n", "scaffold3_cov83 208 210 5.128205\n", "scaffold3_cov83 243 245 2.272727\n", "scaffold3_cov83 261 263 6.666667\n", "scaffold3_cov83 484 486 4.444444\n", "\n", "==> Meth4_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth <==\n", "scaffold6_cov64 2536 2538 0.000000\n", "scaffold6_cov64 2584 2586 0.000000\n", "scaffold6_cov64 4588 4590 0.000000\n", "scaffold6_cov64 5101 5103 0.000000\n", "scaffold6_cov64 5309 5311 0.000000\n", "scaffold6_cov64 5456 5458 0.000000\n", "scaffold6_cov64 5486 5488 0.000000\n", "scaffold6_cov64 5545 5547 0.000000\n", "scaffold6_cov64 5559 5561 0.000000\n", "scaffold6_cov64 5561 5563 2.941176\n", "\n", "==> Meth5_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth <==\n", "scaffold6_cov64 2584 2586 0.000000\n", "scaffold6_cov64 2682 2684 0.000000\n", "scaffold6_cov64 4588 4590 0.000000\n", "scaffold6_cov64 5559 5561 7.692308\n", "scaffold6_cov64 5561 5563 7.142857\n", "scaffold6_cov64 5567 5569 0.000000\n", "scaffold6_cov64 5574 5576 5.263158\n", "scaffold6_cov64 5581 5583 0.000000\n", "scaffold6_cov64 5583 5585 0.000000\n", "scaffold6_cov64 5592 5594 0.000000\n", "\n", "==> Meth6_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth <==\n", "scaffold6_cov64 5456 5458 0.000000\n", "scaffold6_cov64 5486 5488 0.000000\n", "scaffold6_cov64 5545 5547 0.000000\n", "scaffold6_cov64 5559 5561 4.166667\n", "scaffold6_cov64 5561 5563 0.000000\n", "scaffold6_cov64 5567 5569 0.000000\n", "scaffold6_cov64 5574 5576 0.000000\n", "scaffold6_cov64 5581 5583 8.333333\n", "scaffold6_cov64 5583 5585 0.000000\n", "scaffold6_cov64 5592 5594 0.000000\n", "\n", "==> Meth7_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth <==\n", "scaffold2_cov51 649 651 0.000000\n", "scaffold2_cov51 686 688 0.000000\n", "scaffold2_cov51 778 780 0.000000\n", "scaffold3_cov83 243 245 0.000000\n", "scaffold6_cov64 290 292 0.000000\n", "scaffold6_cov64 298 300 0.000000\n", "scaffold6_cov64 489 491 0.000000\n", "scaffold6_cov64 2179 2181 0.000000\n", "scaffold6_cov64 2872 2874 0.000000\n", "scaffold6_cov64 2876 2878 0.000000\n", "\n", "==> Meth8_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth <==\n", "scaffold3_cov83 243 245 0.000000\n", "scaffold6_cov64 290 292 0.000000\n", "scaffold6_cov64 298 300 0.000000\n", "scaffold6_cov64 5101 5103 0.000000\n", "scaffold6_cov64 5545 5547 0.000000\n", "scaffold6_cov64 5559 5561 0.000000\n", "scaffold6_cov64 5561 5563 0.000000\n", "scaffold6_cov64 5567 5569 0.000000\n", "scaffold6_cov64 5574 5576 0.000000\n", "scaffold6_cov64 5581 5583 0.000000\n", "\n", "==> Meth9_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth <==\n", "scaffold3_cov83 243 245 0.000000\n", "scaffold6_cov64 290 292 0.000000\n", "scaffold6_cov64 298 300 0.000000\n", "scaffold6_cov64 489 491 0.000000\n", "scaffold6_cov64 826 828 0.000000\n", "scaffold6_cov64 2097 2099 0.000000\n", "scaffold6_cov64 2179 2181 0.000000\n", "scaffold6_cov64 2805 2807 0.000000\n", "scaffold6_cov64 3198 3200 0.000000\n", "scaffold6_cov64 3343 3345 0.000000\n" ] } ], "source": [ "!head *unMeth" ] }, { "cell_type": "code", "execution_count": 183, "metadata": { "collapsed": false, "scrolled": true }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ " 5068668 Meth1_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth\n", " 5886395 Meth2_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth\n", " 5356621 Meth3_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth\n", " 1666814 Meth4_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth\n", " 1356047 Meth5_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth\n", " 1401495 Meth6_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth\n", " 2086344 Meth7_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth\n", " 245580 Meth8_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth\n", " 2139382 Meth9_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth\n", " 25207346 total\n" ] } ], "source": [ "!wc -l *unMeth" ] }, { "cell_type": "code", "execution_count": 184, "metadata": { "collapsed": true }, "outputs": [], "source": [ "!wc -l *-unMeth > Pact-5x-unMeth-counts.txt" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "### 4. Characterize genomic locations of CpGs" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "#### 4a. Create BEDfiles" ] }, { "cell_type": "code", "execution_count": 185, "metadata": { "collapsed": false, "scrolled": true }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ " 5546051 Meth1_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed\n", " 6358722 Meth2_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed\n", " 5866786 Meth3_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed\n", " 1835561 Meth4_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed\n", " 1451229 Meth5_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed\n", " 1517358 Meth6_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed\n", " 2640625 Meth7_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed\n", " 539008 Meth8_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed\n", " 2732607 Meth9_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed\n" ] } ], "source": [ "%%bash\n", "\n", "for f in *bedgraph\n", "do\n", " awk '{print $1\"\\t\"$2\"\\t\"$3\"\\t\"$4}' ${f} > ${f}.bed\n", " wc -l ${f}.bed\n", "done" ] }, { "cell_type": "code", "execution_count": 186, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ " 110364 Meth1_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed\n", " 126440 Meth2_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed\n", " 124819 Meth3_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed\n", " 31047 Meth4_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed\n", " 30345 Meth5_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed\n", " 26617 Meth6_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed\n", " 258222 Meth7_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed\n", " 213342 Meth8_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed\n", " 255370 Meth9_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed\n" ] } ], "source": [ "%%bash\n", "\n", "for f in *bedgraph-Meth\n", "do\n", " awk '{print $1\"\\t\"$2\"\\t\"$3\"\\t\"$4}' ${f} > ${f}.bed\n", " wc -l ${f}.bed\n", "done" ] }, { "cell_type": "code", "execution_count": 187, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ " 367019 Meth1_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed\n", " 345887 Meth2_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed\n", " 385346 Meth3_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed\n", " 137700 Meth4_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed\n", " 64837 Meth5_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed\n", " 89246 Meth6_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed\n", " 296059 Meth7_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed\n", " 80086 Meth8_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed\n", " 337855 Meth9_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed\n" ] } ], "source": [ "%%bash\n", "\n", "for f in *bedgraph-sparseMeth\n", "do\n", " awk '{print $1\"\\t\"$2\"\\t\"$3\"\\t\"$4}' ${f} > ${f}.bed\n", " wc -l ${f}.bed\n", "done" ] }, { "cell_type": "code", "execution_count": 188, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ " 5068668 Meth1_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed\n", " 5886395 Meth2_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed\n", " 5356621 Meth3_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed\n", " 1666814 Meth4_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed\n", " 1356047 Meth5_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed\n", " 1401495 Meth6_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed\n", " 2086344 Meth7_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed\n", " 245580 Meth8_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed\n", " 2139382 Meth9_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed\n" ] } ], "source": [ "%%bash\n", "\n", "for f in *bedgraph-unMeth\n", "do\n", " awk '{print $1\"\\t\"$2\"\\t\"$3\"\\t\"$4}' ${f} > ${f}.bed\n", " wc -l ${f}.bed\n", "done" ] }, { "cell_type": "code", "execution_count": 189, "metadata": { "collapsed": false, "scrolled": true }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "Meth1_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed\r\n", "Meth1_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed\r\n", "Meth1_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed\r\n", "Meth1_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed\r\n", "Meth2_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed\r\n", "Meth2_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed\r\n", "Meth2_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed\r\n", "Meth2_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed\r\n", "Meth3_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed\r\n", "Meth3_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed\r\n", "Meth3_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed\r\n", "Meth3_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed\r\n", "Meth4_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed\r\n", "Meth4_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed\r\n", "Meth4_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed\r\n", "Meth4_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed\r\n", "Meth5_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed\r\n", "Meth5_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed\r\n", "Meth5_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed\r\n", "Meth5_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed\r\n", "Meth6_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed\r\n", "Meth6_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed\r\n", "Meth6_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed\r\n", "Meth6_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed\r\n", "Meth7_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed\r\n", "Meth7_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed\r\n", "Meth7_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed\r\n", "Meth7_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed\r\n", "Meth8_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed\r\n", "Meth8_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed\r\n", "Meth8_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed\r\n", "Meth8_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed\r\n", "Meth9_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed\r\n", "Meth9_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed\r\n", "Meth9_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed\r\n", "Meth9_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed\r\n" ] } ], "source": [ "#Confirm BEDfile creation\n", "!find *.bed" ] }, { "cell_type": "code", "execution_count": 190, "metadata": { "collapsed": false, "scrolled": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "scaffold1_cov55\t102\t104\t16.666667\r\n", "scaffold1_cov55\t105\t107\t0.000000\r\n", "scaffold1_cov55\t116\t118\t0.000000\r\n", "scaffold1_cov55\t119\t121\t0.000000\r\n", "scaffold1_cov55\t146\t148\t0.000000\r\n", "scaffold1_cov55\t186\t188\t20.000000\r\n", "scaffold1_cov55\t194\t196\t0.000000\r\n", "scaffold2_cov51\t649\t651\t0.000000\r\n", "scaffold2_cov51\t686\t688\t8.333333\r\n", "scaffold2_cov51\t778\t780\t0.000000\r\n" ] } ], "source": [ "#Confirm file creation\n", "!head Meth1_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "#### 4b. Genes" ] }, { "cell_type": "code", "execution_count": 191, "metadata": { "collapsed": true, "scrolled": true }, "outputs": [], "source": [ "%%bash\n", "\n", "for f in *bed\n", "do\n", " /usr/local/bin/intersectBed \\\n", " -u \\\n", " -a ${f} \\\n", " -b ../../../genome-feature-files/Pact.GFFannotation.Genes.gff \\\n", " > ${f}-paGenes\n", "done" ] }, { "cell_type": "code", "execution_count": 192, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "==> Meth1_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-paGenes <==\r\n", "scaffold7_cov100\t4351\t4353\t50.000000\r\n", "scaffold7_cov100\t5500\t5502\t83.333333\r\n", "scaffold7_cov100\t5578\t5580\t57.142857\r\n", "scaffold7_cov100\t5986\t5988\t100.000000\r\n", "scaffold7_cov100\t6144\t6146\t100.000000\r\n", "scaffold7_cov100\t6188\t6190\t100.000000\r\n", "scaffold7_cov100\t6198\t6200\t88.888889\r\n", "scaffold7_cov100\t7438\t7440\t100.000000\r\n", "scaffold7_cov100\t7696\t7698\t100.000000\r\n", "scaffold7_cov100\t7796\t7798\t100.000000\r\n", "\r\n", "==> Meth1_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-paGenes <==\r\n", "scaffold7_cov100\t1293\t1295\t11.111111\r\n", "scaffold7_cov100\t2173\t2175\t11.111111\r\n", "scaffold7_cov100\t2289\t2291\t13.333333\r\n", "scaffold7_cov100\t3713\t3715\t16.666667\r\n", "scaffold7_cov100\t3870\t3872\t11.111111\r\n", "scaffold7_cov100\t4481\t4483\t20.000000\r\n", "scaffold7_cov100\t4596\t4598\t12.500000\r\n", "scaffold7_cov100\t9715\t9717\t18.181818\r\n", "scaffold7_cov100\t11439\t11441\t44.444444\r\n", "scaffold7_cov100\t13441\t13443\t20.000000\r\n", "\r\n", "==> Meth1_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-paGenes <==\r\n", "scaffold6_cov64\t167\t169\t0.000000\r\n", "scaffold6_cov64\t290\t292\t0.000000\r\n", "scaffold6_cov64\t298\t300\t0.000000\r\n", "scaffold6_cov64\t489\t491\t0.000000\r\n", "scaffold6_cov64\t826\t828\t0.000000\r\n", "scaffold6_cov64\t1539\t1541\t0.000000\r\n", "scaffold6_cov64\t1725\t1727\t0.000000\r\n", "scaffold6_cov64\t2097\t2099\t0.000000\r\n", "scaffold6_cov64\t2179\t2181\t8.333333\r\n", "scaffold6_cov64\t2253\t2255\t0.000000\r\n", "\r\n", "==> Meth1_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-paGenes <==\r\n", "scaffold6_cov64\t167\t169\t0.000000\r\n", "scaffold6_cov64\t290\t292\t0.000000\r\n", "scaffold6_cov64\t298\t300\t0.000000\r\n", "scaffold6_cov64\t489\t491\t0.000000\r\n", "scaffold6_cov64\t826\t828\t0.000000\r\n", "scaffold6_cov64\t1539\t1541\t0.000000\r\n", "scaffold6_cov64\t1725\t1727\t0.000000\r\n", "scaffold6_cov64\t2097\t2099\t0.000000\r\n", "scaffold6_cov64\t2179\t2181\t8.333333\r\n", "scaffold6_cov64\t2253\t2255\t0.000000\r\n", "\r\n", "==> Meth2_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-paGenes <==\r\n", "scaffold7_cov100\t5500\t5502\t62.500000\r\n", "scaffold7_cov100\t5986\t5988\t66.666667\r\n", "scaffold7_cov100\t6144\t6146\t100.000000\r\n", "scaffold7_cov100\t6188\t6190\t94.117647\r\n", "scaffold7_cov100\t6198\t6200\t100.000000\r\n", "scaffold7_cov100\t7438\t7440\t88.235294\r\n", "scaffold7_cov100\t7696\t7698\t95.833333\r\n", "scaffold7_cov100\t7796\t7798\t60.000000\r\n", "scaffold7_cov100\t7891\t7893\t96.153846\r\n", "scaffold7_cov100\t9877\t9879\t75.000000\r\n", "\r\n", "==> Meth2_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-paGenes <==\r\n", "scaffold6_cov64\t3978\t3980\t11.111111\r\n", "scaffold7_cov100\t3994\t3996\t10.526316\r\n", "scaffold7_cov100\t7121\t7123\t25.000000\r\n", "scaffold7_cov100\t7201\t7203\t16.666667\r\n", "scaffold7_cov100\t10755\t10757\t13.333333\r\n", "scaffold7_cov100\t11439\t11441\t40.000000\r\n", "scaffold7_cov100\t13385\t13387\t18.750000\r\n", "scaffold7_cov100\t15312\t15314\t16.666667\r\n", "scaffold7_cov100\t15455\t15457\t11.111111\r\n", "scaffold7_cov100\t16874\t16876\t18.181818\r\n", "\r\n", "==> Meth2_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-paGenes <==\r\n", "scaffold6_cov64\t167\t169\t0.000000\r\n", "scaffold6_cov64\t290\t292\t5.000000\r\n", "scaffold6_cov64\t298\t300\t0.000000\r\n", "scaffold6_cov64\t489\t491\t0.000000\r\n", "scaffold6_cov64\t826\t828\t0.000000\r\n", "scaffold6_cov64\t1539\t1541\t0.000000\r\n", "scaffold6_cov64\t1725\t1727\t0.000000\r\n", "scaffold6_cov64\t2097\t2099\t0.000000\r\n", "scaffold6_cov64\t2179\t2181\t0.000000\r\n", "scaffold6_cov64\t2253\t2255\t0.000000\r\n", "\r\n", "==> Meth2_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-paGenes <==\r\n", "scaffold6_cov64\t167\t169\t0.000000\r\n", "scaffold6_cov64\t290\t292\t5.000000\r\n", "scaffold6_cov64\t298\t300\t0.000000\r\n", "scaffold6_cov64\t489\t491\t0.000000\r\n", "scaffold6_cov64\t826\t828\t0.000000\r\n", "scaffold6_cov64\t1539\t1541\t0.000000\r\n", "scaffold6_cov64\t1725\t1727\t0.000000\r\n", "scaffold6_cov64\t2097\t2099\t0.000000\r\n", "scaffold6_cov64\t2179\t2181\t0.000000\r\n", "scaffold6_cov64\t2253\t2255\t0.000000\r\n", "\r\n", "==> Meth3_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-paGenes <==\r\n", "scaffold7_cov100\t5500\t5502\t87.500000\r\n", "scaffold7_cov100\t5578\t5580\t55.555556\r\n", "scaffold7_cov100\t5986\t5988\t60.000000\r\n", "scaffold7_cov100\t6144\t6146\t100.000000\r\n", "scaffold7_cov100\t6188\t6190\t100.000000\r\n", "scaffold7_cov100\t6198\t6200\t100.000000\r\n", "scaffold7_cov100\t7438\t7440\t100.000000\r\n", "scaffold7_cov100\t7696\t7698\t100.000000\r\n", "scaffold7_cov100\t7796\t7798\t81.818182\r\n", "scaffold7_cov100\t7891\t7893\t100.000000\r\n", "\r\n", "==> Meth3_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-paGenes <==\r\n", "scaffold6_cov64\t1725\t1727\t11.111111\r\n", "scaffold6_cov64\t3533\t3535\t14.285714\r\n", "scaffold6_cov64\t5904\t5906\t12.500000\r\n", "scaffold6_cov64\t5992\t5994\t12.500000\r\n", "scaffold7_cov100\t1535\t1537\t12.500000\r\n", "scaffold7_cov100\t4305\t4307\t33.333333\r\n", "scaffold7_cov100\t4351\t4353\t14.285714\r\n", "scaffold7_cov100\t4630\t4632\t28.000000\r\n", "scaffold7_cov100\t4678\t4680\t13.333333\r\n", "scaffold7_cov100\t7121\t7123\t12.500000\r\n", "\r\n", "==> Meth3_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-paGenes <==\r\n", "scaffold6_cov64\t167\t169\t0.000000\r\n", "scaffold6_cov64\t290\t292\t0.000000\r\n", "scaffold6_cov64\t298\t300\t0.000000\r\n", "scaffold6_cov64\t489\t491\t0.000000\r\n", "scaffold6_cov64\t826\t828\t6.250000\r\n", "scaffold6_cov64\t2097\t2099\t0.000000\r\n", "scaffold6_cov64\t2179\t2181\t0.000000\r\n", "scaffold6_cov64\t2253\t2255\t0.000000\r\n", "scaffold6_cov64\t2386\t2388\t0.000000\r\n", "scaffold6_cov64\t2676\t2678\t0.000000\r\n", "\r\n", "==> Meth3_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-paGenes <==\r\n", "scaffold6_cov64\t167\t169\t0.000000\r\n", "scaffold6_cov64\t290\t292\t0.000000\r\n", "scaffold6_cov64\t298\t300\t0.000000\r\n", "scaffold6_cov64\t489\t491\t0.000000\r\n", "scaffold6_cov64\t826\t828\t6.250000\r\n", "scaffold6_cov64\t1725\t1727\t11.111111\r\n", "scaffold6_cov64\t2097\t2099\t0.000000\r\n", "scaffold6_cov64\t2179\t2181\t0.000000\r\n", "scaffold6_cov64\t2253\t2255\t0.000000\r\n", "scaffold6_cov64\t2386\t2388\t0.000000\r\n", "\r\n", "==> Meth4_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-paGenes <==\r\n", "scaffold7_cov100\t1535\t1537\t60.000000\r\n", "scaffold7_cov100\t33140\t33142\t80.000000\r\n", "scaffold7_cov100\t33157\t33159\t80.000000\r\n", "scaffold7_cov100\t96791\t96793\t65.000000\r\n", "scaffold7_cov100\t109716\t109718\t60.000000\r\n", "scaffold7_cov100\t138357\t138359\t100.000000\r\n", "scaffold7_cov100\t138372\t138374\t100.000000\r\n", "scaffold7_cov100\t138390\t138392\t100.000000\r\n", "scaffold7_cov100\t201089\t201091\t60.000000\r\n", "scaffold7_cov100\t201104\t201106\t60.000000\r\n", "\r\n", "==> Meth4_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-paGenes <==\r\n", "scaffold6_cov64\t2676\t2678\t20.000000\r\n", "scaffold6_cov64\t5904\t5906\t15.485564\r\n", "scaffold7_cov100\t1618\t1620\t12.500000\r\n", "scaffold7_cov100\t1628\t1630\t14.285714\r\n", "scaffold7_cov100\t4351\t4353\t46.428571\r\n", "scaffold7_cov100\t15408\t15410\t20.000000\r\n", "scaffold7_cov100\t46343\t46345\t21.739130\r\n", "scaffold7_cov100\t46397\t46399\t12.500000\r\n", "scaffold7_cov100\t46898\t46900\t20.000000\r\n", "scaffold7_cov100\t48729\t48731\t28.571429\r\n", "\r\n", "==> Meth4_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-paGenes <==\r\n", "scaffold6_cov64\t2536\t2538\t0.000000\r\n", "scaffold6_cov64\t2584\t2586\t0.000000\r\n", "scaffold6_cov64\t4588\t4590\t0.000000\r\n", "scaffold6_cov64\t5101\t5103\t0.000000\r\n", "scaffold6_cov64\t5309\t5311\t0.000000\r\n", "scaffold6_cov64\t5456\t5458\t0.000000\r\n", "scaffold6_cov64\t5486\t5488\t0.000000\r\n", "scaffold6_cov64\t5545\t5547\t0.000000\r\n", "scaffold6_cov64\t5559\t5561\t0.000000\r\n", "scaffold6_cov64\t5561\t5563\t2.941176\r\n", "\r\n", "==> Meth4_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-paGenes <==\r\n", "scaffold6_cov64\t2536\t2538\t0.000000\r\n", "scaffold6_cov64\t2584\t2586\t0.000000\r\n", "scaffold6_cov64\t2676\t2678\t20.000000\r\n", "scaffold6_cov64\t4588\t4590\t0.000000\r\n", "scaffold6_cov64\t5101\t5103\t0.000000\r\n", "scaffold6_cov64\t5309\t5311\t0.000000\r\n", "scaffold6_cov64\t5456\t5458\t0.000000\r\n", "scaffold6_cov64\t5486\t5488\t0.000000\r\n", "scaffold6_cov64\t5545\t5547\t0.000000\r\n", "scaffold6_cov64\t5559\t5561\t0.000000\r\n", "\r\n", "==> Meth5_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-paGenes <==\r\n", "scaffold6_cov64\t2676\t2678\t77.777778\r\n", "scaffold7_cov100\t2301\t2303\t50.000000\r\n", "scaffold7_cov100\t17000\t17002\t100.000000\r\n", "scaffold7_cov100\t17090\t17092\t100.000000\r\n", "scaffold7_cov100\t61080\t61082\t57.142857\r\n", "scaffold7_cov100\t69126\t69128\t80.000000\r\n", "scaffold7_cov100\t96721\t96723\t83.333333\r\n", "scaffold7_cov100\t96740\t96742\t71.428571\r\n", "scaffold7_cov100\t96787\t96789\t52.631579\r\n", "scaffold7_cov100\t96791\t96793\t60.000000\r\n", "\r\n", "==> Meth5_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-paGenes <==\r\n", "scaffold6_cov64\t4553\t4555\t20.000000\r\n", "scaffold6_cov64\t5545\t5547\t14.285714\r\n", "scaffold6_cov64\t6374\t6376\t45.454545\r\n", "scaffold7_cov100\t17074\t17076\t33.333333\r\n", "scaffold7_cov100\t17098\t17100\t20.000000\r\n", "scaffold7_cov100\t36543\t36545\t25.000000\r\n", "scaffold7_cov100\t36600\t36602\t25.000000\r\n", "scaffold7_cov100\t46343\t46345\t46.153846\r\n", "scaffold7_cov100\t46428\t46430\t14.285714\r\n", "scaffold7_cov100\t94139\t94141\t27.272727\r\n", "\r\n", "==> Meth5_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-paGenes <==\r\n", "scaffold6_cov64\t2584\t2586\t0.000000\r\n", "scaffold6_cov64\t2682\t2684\t0.000000\r\n", "scaffold6_cov64\t4588\t4590\t0.000000\r\n", "scaffold6_cov64\t5559\t5561\t7.692308\r\n", "scaffold6_cov64\t5561\t5563\t7.142857\r\n", "scaffold6_cov64\t5567\t5569\t0.000000\r\n", "scaffold6_cov64\t5574\t5576\t5.263158\r\n", "scaffold6_cov64\t5581\t5583\t0.000000\r\n", "scaffold6_cov64\t5583\t5585\t0.000000\r\n", "scaffold6_cov64\t5592\t5594\t0.000000\r\n", "\r\n", "==> Meth5_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-paGenes <==\r\n", "scaffold6_cov64\t2584\t2586\t0.000000\r\n", "scaffold6_cov64\t2676\t2678\t77.777778\r\n", "scaffold6_cov64\t2682\t2684\t0.000000\r\n", "scaffold6_cov64\t4553\t4555\t20.000000\r\n", "scaffold6_cov64\t4588\t4590\t0.000000\r\n", "scaffold6_cov64\t5545\t5547\t14.285714\r\n", "scaffold6_cov64\t5559\t5561\t7.692308\r\n", "scaffold6_cov64\t5561\t5563\t7.142857\r\n", "scaffold6_cov64\t5567\t5569\t0.000000\r\n", "scaffold6_cov64\t5574\t5576\t5.263158\r\n", "\r\n", "==> Meth6_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-paGenes <==\r\n", "scaffold7_cov100\t106242\t106244\t66.666667\r\n", "scaffold7_cov100\t106251\t106253\t66.666667\r\n", "scaffold7_cov100\t106254\t106256\t66.666667\r\n", "scaffold7_cov100\t138357\t138359\t50.000000\r\n", "scaffold7_cov100\t138372\t138374\t100.000000\r\n", "scaffold7_cov100\t138390\t138392\t100.000000\r\n", "scaffold7_cov100\t277720\t277722\t100.000000\r\n", "scaffold7_cov100\t346786\t346788\t53.333333\r\n", "scaffold7_cov100\t360165\t360167\t100.000000\r\n", "scaffold7_cov100\t383785\t383787\t60.000000\r\n", "\r\n", "==> Meth6_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-paGenes <==\r\n", "scaffold6_cov64\t4553\t4555\t14.285714\r\n", "scaffold6_cov64\t4588\t4590\t22.222222\r\n", "scaffold6_cov64\t5604\t5606\t11.538462\r\n", "scaffold6_cov64\t6266\t6268\t14.285714\r\n", "scaffold6_cov64\t6374\t6376\t20.000000\r\n", "scaffold7_cov100\t4351\t4353\t10.256410\r\n", "scaffold7_cov100\t32521\t32523\t18.750000\r\n", "scaffold7_cov100\t32984\t32986\t13.333333\r\n", "scaffold7_cov100\t37484\t37486\t16.666667\r\n", "scaffold7_cov100\t37506\t37508\t16.666667\r\n", "\r\n", "==> Meth6_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-paGenes <==\r\n", "scaffold6_cov64\t5456\t5458\t0.000000\r\n", "scaffold6_cov64\t5486\t5488\t0.000000\r\n", "scaffold6_cov64\t5545\t5547\t0.000000\r\n", "scaffold6_cov64\t5559\t5561\t4.166667\r\n", "scaffold6_cov64\t5561\t5563\t0.000000\r\n", "scaffold6_cov64\t5567\t5569\t0.000000\r\n", "scaffold6_cov64\t5574\t5576\t0.000000\r\n", "scaffold6_cov64\t5581\t5583\t8.333333\r\n", "scaffold6_cov64\t5583\t5585\t0.000000\r\n", "scaffold6_cov64\t5592\t5594\t0.000000\r\n", "\r\n", "==> Meth6_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-paGenes <==\r\n", "scaffold6_cov64\t4553\t4555\t14.285714\r\n", "scaffold6_cov64\t4588\t4590\t22.222222\r\n", "scaffold6_cov64\t5456\t5458\t0.000000\r\n", "scaffold6_cov64\t5486\t5488\t0.000000\r\n", "scaffold6_cov64\t5545\t5547\t0.000000\r\n", "scaffold6_cov64\t5559\t5561\t4.166667\r\n", "scaffold6_cov64\t5561\t5563\t0.000000\r\n", "scaffold6_cov64\t5567\t5569\t0.000000\r\n", "scaffold6_cov64\t5574\t5576\t0.000000\r\n", "scaffold6_cov64\t5581\t5583\t8.333333\r\n", "\r\n", "==> Meth7_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-paGenes <==\r\n", "scaffold7_cov100\t5500\t5502\t70.000000\r\n", "scaffold7_cov100\t5986\t5988\t73.333333\r\n", "scaffold7_cov100\t6144\t6146\t96.666667\r\n", "scaffold7_cov100\t6188\t6190\t93.181818\r\n", "scaffold7_cov100\t6198\t6200\t95.454545\r\n", "scaffold7_cov100\t7438\t7440\t100.000000\r\n", "scaffold7_cov100\t7696\t7698\t87.500000\r\n", "scaffold7_cov100\t7796\t7798\t95.454545\r\n", "scaffold7_cov100\t7891\t7893\t100.000000\r\n", "scaffold7_cov100\t9715\t9717\t60.000000\r\n", "\r\n", "==> Meth7_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-paGenes <==\r\n", "scaffold6_cov64\t4146\t4148\t20.000000\r\n", "scaffold6_cov64\t5561\t5563\t14.285714\r\n", "scaffold6_cov64\t5644\t5646\t11.111111\r\n", "scaffold7_cov100\t1422\t1424\t33.333333\r\n", "scaffold7_cov100\t1651\t1653\t14.285714\r\n", "scaffold7_cov100\t2080\t2082\t11.111111\r\n", "scaffold7_cov100\t3629\t3631\t12.500000\r\n", "scaffold7_cov100\t5578\t5580\t42.857143\r\n", "scaffold7_cov100\t11439\t11441\t25.000000\r\n", "scaffold7_cov100\t14042\t14044\t18.518519\r\n", "\r\n", "==> Meth7_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-paGenes <==\r\n", "scaffold6_cov64\t290\t292\t0.000000\r\n", "scaffold6_cov64\t298\t300\t0.000000\r\n", "scaffold6_cov64\t489\t491\t0.000000\r\n", "scaffold6_cov64\t2179\t2181\t0.000000\r\n", "scaffold6_cov64\t2872\t2874\t0.000000\r\n", "scaffold6_cov64\t2876\t2878\t0.000000\r\n", "scaffold6_cov64\t3198\t3200\t0.000000\r\n", "scaffold6_cov64\t3343\t3345\t0.000000\r\n", "scaffold6_cov64\t3397\t3399\t0.000000\r\n", "scaffold6_cov64\t3412\t3414\t0.000000\r\n", "\r\n", "==> Meth7_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-paGenes <==\r\n", "scaffold6_cov64\t290\t292\t0.000000\r\n", "scaffold6_cov64\t298\t300\t0.000000\r\n", "scaffold6_cov64\t489\t491\t0.000000\r\n", "scaffold6_cov64\t2179\t2181\t0.000000\r\n", "scaffold6_cov64\t2872\t2874\t0.000000\r\n", "scaffold6_cov64\t2876\t2878\t0.000000\r\n", "scaffold6_cov64\t3198\t3200\t0.000000\r\n", "scaffold6_cov64\t3343\t3345\t0.000000\r\n", "scaffold6_cov64\t3397\t3399\t0.000000\r\n", "scaffold6_cov64\t3412\t3414\t0.000000\r\n", "\r\n", "==> Meth8_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-paGenes <==\r\n", "scaffold7_cov100\t5986\t5988\t78.947368\r\n", "scaffold7_cov100\t6144\t6146\t95.918367\r\n", "scaffold7_cov100\t6188\t6190\t100.000000\r", "\r\n", "scaffold7_cov100\t6198\t6200\t97.297297\r\n", "scaffold7_cov100\t7696\t7698\t100.000000\r\n", "scaffold7_cov100\t7796\t7798\t72.727273\r\n", "scaffold7_cov100\t7891\t7893\t90.000000\r\n", "scaffold7_cov100\t10216\t10218\t85.714286\r\n", "scaffold7_cov100\t10273\t10275\t100.000000\r\n", "scaffold7_cov100\t16831\t16833\t75.000000\r\n", "\r\n", "==> Meth8_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-paGenes <==\r\n", "scaffold6_cov64\t826\t828\t14.285714\r\n", "scaffold7_cov100\t5500\t5502\t11.764706\r\n", "scaffold7_cov100\t7438\t7440\t40.000000\r\n", "scaffold7_cov100\t13385\t13387\t46.666667\r\n", "scaffold7_cov100\t14083\t14085\t40.000000\r\n", "scaffold7_cov100\t16559\t16561\t20.000000\r\n", "scaffold7_cov100\t22257\t22259\t20.000000\r\n", "scaffold7_cov100\t34847\t34849\t20.000000\r\n", "scaffold7_cov100\t41743\t41745\t16.666667\r\n", "scaffold7_cov100\t46132\t46134\t16.666667\r\n", "\r\n", "==> Meth8_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-paGenes <==\r\n", "scaffold6_cov64\t290\t292\t0.000000\r\n", "scaffold6_cov64\t298\t300\t0.000000\r\n", "scaffold6_cov64\t5101\t5103\t0.000000\r\n", "scaffold6_cov64\t5545\t5547\t0.000000\r\n", "scaffold6_cov64\t5559\t5561\t0.000000\r\n", "scaffold6_cov64\t5561\t5563\t0.000000\r\n", "scaffold6_cov64\t5567\t5569\t0.000000\r\n", "scaffold6_cov64\t5574\t5576\t0.000000\r\n", "scaffold6_cov64\t5581\t5583\t0.000000\r\n", "scaffold6_cov64\t6183\t6185\t0.000000\r\n", "\r\n", "==> Meth8_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-paGenes <==\r\n", "scaffold6_cov64\t290\t292\t0.000000\r\n", "scaffold6_cov64\t298\t300\t0.000000\r\n", "scaffold6_cov64\t826\t828\t14.285714\r\n", "scaffold6_cov64\t5101\t5103\t0.000000\r\n", "scaffold6_cov64\t5545\t5547\t0.000000\r\n", "scaffold6_cov64\t5559\t5561\t0.000000\r\n", "scaffold6_cov64\t5561\t5563\t0.000000\r\n", "scaffold6_cov64\t5567\t5569\t0.000000\r\n", "scaffold6_cov64\t5574\t5576\t0.000000\r\n", "scaffold6_cov64\t5581\t5583\t0.000000\r\n", "\r\n", "==> Meth9_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-paGenes <==\r\n", "scaffold7_cov100\t5578\t5580\t66.666667\r\n", "scaffold7_cov100\t5986\t5988\t79.166667\r\n", "scaffold7_cov100\t6144\t6146\t96.296296\r\n", "scaffold7_cov100\t6188\t6190\t92.592593\r\n", "scaffold7_cov100\t6198\t6200\t94.339623\r\n", "scaffold7_cov100\t7201\t7203\t80.000000\r\n", "scaffold7_cov100\t7438\t7440\t100.000000\r\n", "scaffold7_cov100\t7696\t7698\t91.304348\r\n", "scaffold7_cov100\t7796\t7798\t100.000000\r\n", "scaffold7_cov100\t7891\t7893\t92.857143\r\n", "\r\n", "==> Meth9_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-paGenes <==\r\n", "scaffold6_cov64\t3435\t3437\t15.384615\r\n", "scaffold6_cov64\t4146\t4148\t12.500000\r\n", "scaffold6_cov64\t5904\t5906\t14.285714\r\n", "scaffold7_cov100\t1390\t1392\t16.666667\r\n", "scaffold7_cov100\t1941\t1943\t12.500000\r\n", "scaffold7_cov100\t2043\t2045\t11.111111\r\n", "scaffold7_cov100\t3956\t3958\t20.000000\r\n", "scaffold7_cov100\t4630\t4632\t25.000000\r\n", "scaffold7_cov100\t4678\t4680\t33.333333\r\n", "scaffold7_cov100\t10755\t10757\t15.000000\r\n", "\r\n", "==> Meth9_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-paGenes <==\r\n", "scaffold6_cov64\t290\t292\t0.000000\r\n", "scaffold6_cov64\t298\t300\t0.000000\r\n", "scaffold6_cov64\t489\t491\t0.000000\r\n", "scaffold6_cov64\t826\t828\t0.000000\r\n", "scaffold6_cov64\t2097\t2099\t0.000000\r\n", "scaffold6_cov64\t2179\t2181\t0.000000\r\n", "scaffold6_cov64\t2805\t2807\t0.000000\r\n", "scaffold6_cov64\t3198\t3200\t0.000000\r\n", "scaffold6_cov64\t3343\t3345\t0.000000\r\n", "scaffold6_cov64\t3397\t3399\t0.000000\r\n", "\r\n", "==> Meth9_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-paGenes <==\r\n", "scaffold6_cov64\t290\t292\t0.000000\r\n", "scaffold6_cov64\t298\t300\t0.000000\r\n", "scaffold6_cov64\t489\t491\t0.000000\r\n", "scaffold6_cov64\t826\t828\t0.000000\r\n", "scaffold6_cov64\t2097\t2099\t0.000000\r\n", "scaffold6_cov64\t2179\t2181\t0.000000\r\n", "scaffold6_cov64\t2805\t2807\t0.000000\r\n", "scaffold6_cov64\t3198\t3200\t0.000000\r\n", "scaffold6_cov64\t3343\t3345\t0.000000\r\n", "scaffold6_cov64\t3397\t3399\t0.000000\r\n" ] } ], "source": [ "#Check output\n", "!head *paGenes" ] }, { "cell_type": "code", "execution_count": 193, "metadata": { "collapsed": false, "scrolled": true }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ " 73903 Meth1_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-paGenes\n", " 157238 Meth1_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-paGenes\n", " 2234075 Meth1_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-paGenes\n", " 2465216 Meth1_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-paGenes\n", " 85798 Meth2_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-paGenes\n", " 144175 Meth2_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-paGenes\n", " 2529901 Meth2_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-paGenes\n", " 2759874 Meth2_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-paGenes\n", " 82312 Meth3_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-paGenes\n", " 161680 Meth3_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-paGenes\n", " 2342437 Meth3_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-paGenes\n", " 2586429 Meth3_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-paGenes\n", " 13574 Meth4_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-paGenes\n", " 56227 Meth4_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-paGenes\n", " 705698 Meth4_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-paGenes\n", " 775499 Meth4_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-paGenes\n", " 12764 Meth5_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-paGenes\n", " 25937 Meth5_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-paGenes\n", " 568019 Meth5_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-paGenes\n", " 606720 Meth5_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-paGenes\n", " 11385 Meth6_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-paGenes\n", " 35609 Meth6_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-paGenes\n", " 592098 Meth6_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-paGenes\n", " 639092 Meth6_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-paGenes\n", " 118165 Meth7_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-paGenes\n", " 120391 Meth7_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-paGenes\n", " 1014446 Meth7_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-paGenes\n", " 1253002 Meth7_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-paGenes\n", " 85966 Meth8_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-paGenes\n", " 27871 Meth8_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-paGenes\n", " 106046 Meth8_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-paGenes\n", " 219883 Meth8_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-paGenes\n", " 125421 Meth9_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-paGenes\n", " 138915 Meth9_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-paGenes\n", " 1016418 Meth9_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-paGenes\n", " 1280754 Meth9_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-paGenes\n", " 25172938 total\n" ] } ], "source": [ "#Count number of overlaps\n", "!wc -l *paGenes" ] }, { "cell_type": "code", "execution_count": 194, "metadata": { "collapsed": true }, "outputs": [], "source": [ "!wc -l *paGenes > Pact-5x-paGenes-counts.txt" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "#### 4c. Coding Sequences (CDS)" ] }, { "cell_type": "code", "execution_count": 195, "metadata": { "collapsed": true, "scrolled": true }, "outputs": [], "source": [ "%%bash\n", "\n", "for f in *bed\n", "do\n", " /usr/local/bin/intersectBed \\\n", " -u \\\n", " -a ${f} \\\n", " -b ../../../genome-feature-files/Pact.GFFannotation.CDS.gff \\\n", " > ${f}-paCDS\n", "done" ] }, { "cell_type": "code", "execution_count": 196, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "==> Meth1_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-paCDS <==\n", "scaffold7_cov100\t5500\t5502\t83.333333\n", "scaffold7_cov100\t6144\t6146\t100.000000\n", "scaffold7_cov100\t6188\t6190\t100.000000\n", "scaffold7_cov100\t6198\t6200\t88.888889\n", "scaffold7_cov100\t7696\t7698\t100.000000\n", "scaffold7_cov100\t7891\t7893\t100.000000\n", "scaffold7_cov100\t8323\t8325\t100.000000\n", "scaffold7_cov100\t9877\t9879\t92.857143\n", "scaffold7_cov100\t10216\t10218\t100.000000\n", "scaffold7_cov100\t10273\t10275\t85.714286\n", "\n", "==> Meth1_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-paCDS <==\n", "scaffold7_cov100\t1293\t1295\t11.111111\n", "scaffold7_cov100\t2173\t2175\t11.111111\n", "scaffold7_cov100\t2289\t2291\t13.333333\n", "scaffold7_cov100\t9715\t9717\t18.181818\n", "scaffold7_cov100\t15428\t15430\t12.500000\n", "scaffold7_cov100\t15440\t15442\t12.500000\n", "scaffold7_cov100\t15455\t15457\t12.500000\n", "scaffold7_cov100\t15963\t15965\t11.111111\n", "scaffold7_cov100\t16023\t16025\t14.285714\n", "scaffold7_cov100\t16283\t16285\t20.000000\n", "\n", "==> Meth1_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-paCDS <==\n", "scaffold6_cov64\t826\t828\t0.000000\n", "scaffold6_cov64\t1539\t1541\t0.000000\n", "scaffold6_cov64\t2097\t2099\t0.000000\n", "scaffold6_cov64\t2179\t2181\t8.333333\n", "scaffold6_cov64\t2253\t2255\t0.000000\n", "scaffold6_cov64\t4793\t4795\t0.000000\n", "scaffold6_cov64\t5581\t5583\t3.030303\n", "scaffold6_cov64\t5583\t5585\t0.000000\n", "scaffold6_cov64\t5592\t5594\t0.000000\n", "scaffold6_cov64\t5594\t5596\t0.000000\n", "\n", "==> Meth1_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-paCDS <==\n", "scaffold6_cov64\t826\t828\t0.000000\n", "scaffold6_cov64\t1539\t1541\t0.000000\n", "scaffold6_cov64\t2097\t2099\t0.000000\n", "scaffold6_cov64\t2179\t2181\t8.333333\n", "scaffold6_cov64\t2253\t2255\t0.000000\n", "scaffold6_cov64\t4793\t4795\t0.000000\n", "scaffold6_cov64\t5581\t5583\t3.030303\n", "scaffold6_cov64\t5583\t5585\t0.000000\n", "scaffold6_cov64\t5592\t5594\t0.000000\n", "scaffold6_cov64\t5594\t5596\t0.000000\n", "\n", "==> Meth2_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-paCDS <==\n", "scaffold7_cov100\t5500\t5502\t62.500000\n", "scaffold7_cov100\t6144\t6146\t100.000000\n", "scaffold7_cov100\t6188\t6190\t94.117647\n", "scaffold7_cov100\t6198\t6200\t100.000000\n", "scaffold7_cov100\t7696\t7698\t95.833333\n", "scaffold7_cov100\t7891\t7893\t96.153846\n", "scaffold7_cov100\t9877\t9879\t75.000000\n", "scaffold7_cov100\t10216\t10218\t84.615385\n", "scaffold7_cov100\t10273\t10275\t92.857143\n", "scaffold7_cov100\t11043\t11045\t88.888889\n", "\n", "==> Meth2_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-paCDS <==\n", "scaffold7_cov100\t10755\t10757\t13.333333\n", "scaffold7_cov100\t15455\t15457\t11.111111\n", "scaffold7_cov100\t16874\t16876\t18.181818\n", "scaffold7_cov100\t17074\t17076\t36.363636\n", "scaffold7_cov100\t17098\t17100\t35.714286\n", "scaffold7_cov100\t17212\t17214\t41.666667\n", "scaffold7_cov100\t19339\t19341\t25.000000\n", "scaffold7_cov100\t29019\t29021\t12.500000\n", "scaffold7_cov100\t41767\t41769\t14.285714\n", "scaffold7_cov100\t46359\t46361\t11.111111\n", "\n", "==> Meth2_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-paCDS <==\n", "scaffold6_cov64\t826\t828\t0.000000\n", "scaffold6_cov64\t1539\t1541\t0.000000\n", "scaffold6_cov64\t2097\t2099\t0.000000\n", "scaffold6_cov64\t2179\t2181\t0.000000\n", "scaffold6_cov64\t2253\t2255\t0.000000\n", "scaffold6_cov64\t4793\t4795\t0.000000\n", "scaffold6_cov64\t5581\t5583\t2.857143\n", "scaffold6_cov64\t5583\t5585\t2.857143\n", "scaffold6_cov64\t5592\t5594\t0.000000\n", "scaffold6_cov64\t5594\t5596\t0.000000\n", "\n", "==> Meth2_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-paCDS <==\n", "scaffold6_cov64\t826\t828\t0.000000\n", "scaffold6_cov64\t1539\t1541\t0.000000\n", "scaffold6_cov64\t2097\t2099\t0.000000\n", "scaffold6_cov64\t2179\t2181\t0.000000\n", "scaffold6_cov64\t2253\t2255\t0.000000\n", "scaffold6_cov64\t4793\t4795\t0.000000\n", "scaffold6_cov64\t5581\t5583\t2.857143\n", "scaffold6_cov64\t5583\t5585\t2.857143\n", "scaffold6_cov64\t5592\t5594\t0.000000\n", "scaffold6_cov64\t5594\t5596\t0.000000\n", "\n", "==> Meth3_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-paCDS <==\n", "scaffold7_cov100\t5500\t5502\t87.500000\n", "scaffold7_cov100\t6144\t6146\t100.000000\n", "scaffold7_cov100\t6188\t6190\t100.000000\n", "scaffold7_cov100\t6198\t6200\t100.000000\n", "scaffold7_cov100\t7696\t7698\t100.000000\n", "scaffold7_cov100\t7891\t7893\t100.000000\n", "scaffold7_cov100\t8323\t8325\t100.000000\n", "scaffold7_cov100\t9877\t9879\t88.888889\n", "scaffold7_cov100\t10216\t10218\t88.888889\n", "scaffold7_cov100\t10273\t10275\t80.000000\n", "\n", "==> Meth3_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-paCDS <==\n", "scaffold6_cov64\t5992\t5994\t12.500000\n", "scaffold7_cov100\t1535\t1537\t12.500000\n", "scaffold7_cov100\t4630\t4632\t28.000000\n", "scaffold7_cov100\t4678\t4680\t13.333333\n", "scaffold7_cov100\t9715\t9717\t30.000000\n", "scaffold7_cov100\t10755\t10757\t25.000000\n", "scaffold7_cov100\t14042\t14044\t40.000000\n", "scaffold7_cov100\t17074\t17076\t25.000000\n", "scaffold7_cov100\t17098\t17100\t25.000000\n", "scaffold7_cov100\t17164\t17166\t25.000000\n", "\n", "==> Meth3_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-paCDS <==\n", "scaffold6_cov64\t826\t828\t6.250000\n", "scaffold6_cov64\t2097\t2099\t0.000000\n", "scaffold6_cov64\t2179\t2181\t0.000000\n", "scaffold6_cov64\t2253\t2255\t0.000000\n", "scaffold6_cov64\t4793\t4795\t0.000000\n", "scaffold6_cov64\t5581\t5583\t0.000000\n", "scaffold6_cov64\t5583\t5585\t2.222222\n", "scaffold6_cov64\t5592\t5594\t2.631579\n", "scaffold6_cov64\t5594\t5596\t0.000000\n", "scaffold6_cov64\t5604\t5606\t0.000000\n", "\n", "==> Meth3_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-paCDS <==\n", "scaffold6_cov64\t826\t828\t6.250000\n", "scaffold6_cov64\t2097\t2099\t0.000000\n", "scaffold6_cov64\t2179\t2181\t0.000000\n", "scaffold6_cov64\t2253\t2255\t0.000000\n", "scaffold6_cov64\t4793\t4795\t0.000000\n", "scaffold6_cov64\t5581\t5583\t0.000000\n", "scaffold6_cov64\t5583\t5585\t2.222222\n", "scaffold6_cov64\t5592\t5594\t2.631579\n", "scaffold6_cov64\t5594\t5596\t0.000000\n", "scaffold6_cov64\t5604\t5606\t0.000000\n", "\n", "==> Meth4_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-paCDS <==\n", "scaffold7_cov100\t1535\t1537\t60.000000\n", "scaffold7_cov100\t33140\t33142\t80.000000\n", "scaffold7_cov100\t33157\t33159\t80.000000\n", "scaffold7_cov100\t96791\t96793\t65.000000\n", "scaffold7_cov100\t138357\t138359\t100.000000\n", "scaffold7_cov100\t138372\t138374\t100.000000\n", "scaffold7_cov100\t138390\t138392\t100.000000\n", "scaffold7_cov100\t338971\t338973\t50.000000\n", "scaffold7_cov100\t360165\t360167\t100.000000\n", "scaffold7_cov100\t384121\t384123\t83.333333\n", "\n", "==> Meth4_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-paCDS <==\n", "scaffold7_cov100\t1618\t1620\t12.500000\n", "scaffold7_cov100\t1628\t1630\t14.285714\n", "scaffold7_cov100\t15408\t15410\t20.000000\n", "scaffold7_cov100\t46343\t46345\t21.739130\n", "scaffold7_cov100\t46397\t46399\t12.500000\n", "scaffold7_cov100\t48729\t48731\t28.571429\n", "scaffold7_cov100\t55479\t55481\t13.333333\n", "scaffold7_cov100\t61080\t61082\t12.500000\n", "scaffold7_cov100\t91941\t91943\t20.000000\n", "scaffold7_cov100\t96787\t96789\t42.857143\n", "\n", "==> Meth4_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-paCDS <==\n", "scaffold6_cov64\t5581\t5583\t0.000000\n", "scaffold6_cov64\t5583\t5585\t0.000000\n", "scaffold6_cov64\t5592\t5594\t0.000000\n", "scaffold6_cov64\t5594\t5596\t0.000000\n", "scaffold6_cov64\t5604\t5606\t0.000000\n", "scaffold6_cov64\t5644\t5646\t3.418803\n", "scaffold6_cov64\t5821\t5823\t0.490540\n", "scaffold6_cov64\t5973\t5975\t0.388350\n", "scaffold6_cov64\t5992\t5994\t0.000000\n", "scaffold6_cov64\t6012\t6014\t0.000000\n", "\n", "==> Meth4_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-paCDS <==\n", "scaffold6_cov64\t5581\t5583\t0.000000\n", "scaffold6_cov64\t5583\t5585\t0.000000\n", "scaffold6_cov64\t5592\t5594\t0.000000\n", "scaffold6_cov64\t5594\t5596\t0.000000\n", "scaffold6_cov64\t5604\t5606\t0.000000\n", "scaffold6_cov64\t5644\t5646\t3.418803\n", "scaffold6_cov64\t5821\t5823\t0.490540\n", "scaffold6_cov64\t5973\t5975\t0.388350\n", "scaffold6_cov64\t5992\t5994\t0.000000\n", "scaffold6_cov64\t6012\t6014\t0.000000\n", "\n", "==> Meth5_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-paCDS <==\n", "scaffold7_cov100\t2301\t2303\t50.000000\n", "scaffold7_cov100\t17000\t17002\t100.000000\n", "scaffold7_cov100\t17090\t17092\t100.000000\n", "scaffold7_cov100\t61080\t61082\t57.142857\n", "scaffold7_cov100\t69126\t69128\t80.000000\n", "scaffold7_cov100\t96787\t96789\t52.631579\n", "scaffold7_cov100\t96791\t96793\t60.000000\n", "scaffold7_cov100\t96859\t96861\t71.428571\n", "scaffold7_cov100\t138357\t138359\t50.000000\n", "scaffold7_cov100\t204124\t204126\t83.333333\n", "\n", "==> Meth5_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-paCDS <==\n", "scaffold7_cov100\t17074\t17076\t33.333333\n", "scaffold7_cov100\t17098\t17100\t20.000000\n", "scaffold7_cov100\t46343\t46345\t46.153846\n", "scaffold7_cov100\t46428\t46430\t14.285714\n", "scaffold7_cov100\t94139\t94141\t27.272727\n", "scaffold7_cov100\t94142\t94144\t16.666667\n", "scaffold7_cov100\t94939\t94941\t36.363636\n", "scaffold7_cov100\t131174\t131176\t11.111111\n", "scaffold7_cov100\t236368\t236370\t13.043478\n", "scaffold7_cov100\t346784\t346786\t40.000000\n", "\n", "==> Meth5_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-paCDS <==\n", "scaffold6_cov64\t5581\t5583\t0.000000\n", "scaffold6_cov64\t5583\t5585\t0.000000\n", "scaffold6_cov64\t5592\t5594\t0.000000\n", "scaffold6_cov64\t5594\t5596\t0.000000\n", "scaffold6_cov64\t5604\t5606\t0.000000\n", "scaffold6_cov64\t5644\t5646\t3.613019\n", "scaffold6_cov64\t5821\t5823\t0.408274\n", "scaffold6_cov64\t5965\t5967\t0.000000\n", "scaffold6_cov64\t5973\t5975\t0.453001\n", "scaffold6_cov64\t5992\t5994\t1.670146\n", "\n", "==> Meth5_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-paCDS <==\n", "scaffold6_cov64\t5581\t5583\t0.000000\n", "scaffold6_cov64\t5583\t5585\t0.000000\n", "scaffold6_cov64\t5592\t5594\t0.000000\n", "scaffold6_cov64\t5594\t5596\t0.000000\n", "scaffold6_cov64\t5604\t5606\t0.000000\n", "scaffold6_cov64\t5644\t5646\t3.613019\n", "scaffold6_cov64\t5821\t5823\t0.408274\n", "scaffold6_cov64\t5965\t5967\t0.000000\n", "scaffold6_cov64\t5973\t5975\t0.453001\n", "scaffold6_cov64\t5992\t5994\t1.670146\n", "\n", "==> Meth6_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-paCDS <==\n", "scaffold7_cov100\t106242\t106244\t66.666667\n", "scaffold7_cov100\t106251\t106253\t66.666667\n", "scaffold7_cov100\t106254\t106256\t66.666667\n", "scaffold7_cov100\t138357\t138359\t50.000000\n", "scaffold7_cov100\t138372\t138374\t100.000000\n", "scaffold7_cov100\t138390\t138392\t100.000000\n", "scaffold7_cov100\t277720\t277722\t100.000000\n", "scaffold7_cov100\t346786\t346788\t53.333333\n", "scaffold7_cov100\t360165\t360167\t100.000000\n", "scaffold7_cov100\t383785\t383787\t60.000000\n", "\n", "==> Meth6_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-paCDS <==\n", "scaffold6_cov64\t5604\t5606\t11.538462\n", "scaffold6_cov64\t6266\t6268\t14.285714\n", "scaffold7_cov100\t32984\t32986\t13.333333\n", "scaffold7_cov100\t46343\t46345\t47.619048\n", "scaffold7_cov100\t61080\t61082\t14.285714\n", "scaffold7_cov100\t94109\t94111\t20.000000\n", "scaffold7_cov100\t94113\t94115\t20.000000\n", "scaffold7_cov100\t96787\t96789\t44.444444\n", "scaffold7_cov100\t96791\t96793\t44.444444\n", "scaffold7_cov100\t113377\t113379\t16.666667\n", "\n", "==> Meth6_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-paCDS <==\n", "scaffold6_cov64\t5581\t5583\t8.333333\n", "scaffold6_cov64\t5583\t5585\t0.000000\n", "scaffold6_cov64\t5592\t5594\t0.000000\n", "scaffold6_cov64\t5594\t5596\t0.000000\n", "scaffold6_cov64\t5644\t5646\t2.728873\n", "scaffold6_cov64\t5821\t5823\t0.392773\n", "scaffold6_cov64\t5965\t5967\t0.000000\n", "scaffold6_cov64\t5973\t5975\t0.451467\n", "scaffold6_cov64\t5992\t5994\t0.420168\n", "scaffold6_cov64\t6159\t6161\t0.000000\n", "\n", "==> Meth6_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-paCDS <==\n", "scaffold6_cov64\t5581\t5583\t8.333333\n", "scaffold6_cov64\t5583\t5585\t0.000000\n", "scaffold6_cov64\t5592\t5594\t0.000000\n", "scaffold6_cov64\t5594\t5596\t0.000000\n", "scaffold6_cov64\t5604\t5606\t11.538462\n", "scaffold6_cov64\t5644\t5646\t2.728873\n", "scaffold6_cov64\t5821\t5823\t0.392773\n", "scaffold6_cov64\t5965\t5967\t0.000000\n", "scaffold6_cov64\t5973\t5975\t0.451467\n", "scaffold6_cov64\t5992\t5994\t0.420168\n", "\n", "==> Meth7_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-paCDS <==\n", "scaffold7_cov100\t5500\t5502\t70.000000\n", "scaffold7_cov100\t6144\t6146\t96.666667\n", "scaffold7_cov100\t6188\t6190\t93.181818\n", "scaffold7_cov100\t6198\t6200\t95.454545\n", "scaffold7_cov100\t7696\t7698\t87.500000\n", "scaffold7_cov100\t7891\t7893\t100.000000\n", "scaffold7_cov100\t9715\t9717\t60.000000\n", "scaffold7_cov100\t9877\t9879\t95.833333\n", "scaffold7_cov100\t10216\t10218\t97.058824\n", "scaffold7_cov100\t10273\t10275\t96.551724\n", "\n", "==> Meth7_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-paCDS <==\n", "scaffold6_cov64\t5644\t5646\t11.111111\n", "scaffold7_cov100\t1422\t1424\t33.333333\n", "scaffold7_cov100\t1651\t1653\t14.285714\n", "scaffold7_cov100\t2080\t2082\t11.111111\n", "scaffold7_cov100\t14042\t14044\t18.518519\n", "scaffold7_cov100\t17952\t17954\t38.297872\n", "scaffold7_cov100\t19493\t19495\t47.826087\n", "scaffold7_cov100\t28638\t28640\t16.666667\n", "scaffold7_cov100\t33157\t33159\t20.000000\n", "scaffold7_cov100\t34550\t34552\t16.666667\n", "\n", "==> Meth7_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-paCDS <==\n", "scaffold6_cov64\t2179\t2181\t0.000000\n", "scaffold6_cov64\t4793\t4795\t0.000000\n", "scaffold6_cov64\t5581\t5583\t0.000000\n", "scaffold6_cov64\t5583\t5585\t0.000000\n", "scaffold6_cov64\t5592\t5594\t0.000000\n", "scaffold6_cov64\t5594\t5596\t0.000000\n", "scaffold6_cov64\t5604\t5606\t0.000000\n", "scaffold6_cov64\t5821\t5823\t9.090909\n", "scaffold6_cov64\t5965\t5967\t0.000000\n", "scaffold6_cov64\t5973\t5975\t0.000000\n", "\n", "==> Meth7_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-paCDS <==\n", "scaffold6_cov64\t2179\t2181\t0.000000\n", "scaffold6_cov64\t4793\t4795\t0.000000\n", "scaffold6_cov64\t5581\t5583\t0.000000\n", "scaffold6_cov64\t5583\t5585\t0.000000\n", "scaffold6_cov64\t5592\t5594\t0.000000\n", "scaffold6_cov64\t5594\t5596\t0.000000\n", "scaffold6_cov64\t5604\t5606\t0.000000\n", "scaffold6_cov64\t5644\t5646\t11.111111\n", "scaffold6_cov64\t5821\t5823\t9.090909\n", "scaffold6_cov64\t5965\t5967\t0.000000\n", "\n", "==> Meth8_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-paCDS <==\n", "scaffold7_cov100\t6144\t6146\t95.918367\n", "scaffold7_cov100\t6188\t6190\t100.000000\n", "scaffold7_cov100\t6198\t6200\t97.297297\n", "scaffold7_cov100\t7696\t7698\t100.000000\n", "scaffold7_cov100\t7891\t7893\t90.000000\n", "scaffold7_cov100\t10216\t10218\t85.714286\n", "scaffold7_cov100\t10273\t10275\t100.000000\n", "scaffold7_cov100\t16831\t16833\t75.000000\n", "scaffold7_cov100\t16910\t16912\t100.000000\n", "scaffold7_cov100\t16940\t16942\t100.000000\n", "\n", "==> Meth8_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-paCDS <==\n", "scaffold6_cov64\t826\t828\t14.285714\n", "scaffold7_cov100\t5500\t5502\t11.764706\n", "scaffold7_cov100\t14083\t14085\t40.000000\n", "scaffold7_cov100\t16559\t16561\t20.000000\n", "scaffold7_cov100\t41743\t41745\t16.666667\n", "scaffold7_cov100\t46132\t46134\t16.666667\n", "scaffold7_cov100\t46294\t46296\t12.500000\n", "scaffold7_cov100\t52752\t52754\t20.000000\n", "scaffold7_cov100\t106796\t106798\t14.285714\n", "scaffold7_cov100\t111368\t111370\t28.571429\n", "\n", "==> Meth8_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-paCDS <==\n", "scaffold6_cov64\t5581\t5583\t0.000000\n", "scaffold6_cov64\t6183\t6185\t0.000000\n", "scaffold6_cov64\t6194\t6196\t0.000000\n", "scaffold6_cov64\t6266\t6268\t0.000000\n", "scaffold7_cov100\t2016\t2018\t0.000000\n", "scaffold7_cov100\t16441\t16443\t0.000000\n", "scaffold7_cov100\t16460\t16462\t0.000000\n", "scaffold7_cov100\t16471\t16473\t0.000000\n", "scaffold7_cov100\t16483\t16485\t0.000000\n", "scaffold7_cov100\t16874\t16876\t0.000000\n", "\n", "==> Meth8_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-paCDS <==\n", "scaffold6_cov64\t826\t828\t14.285714\n", "scaffold6_cov64\t5581\t5583\t0.000000\n", "scaffold6_cov64\t6183\t6185\t0.000000\n", "scaffold6_cov64\t6194\t6196\t0.000000\n", "scaffold6_cov64\t6266\t6268\t0.000000\n", "scaffold7_cov100\t2016\t2018\t0.000000\n", "scaffold7_cov100\t5500\t5502\t11.764706\n", "scaffold7_cov100\t6144\t6146\t95.918367\n", "scaffold7_cov100\t6188\t6190\t100.000000\n", "scaffold7_cov100\t6198\t6200\t97.297297\n", "\n", "==> Meth9_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-paCDS <==\n", "scaffold7_cov100\t6144\t6146\t96.296296\n", "scaffold7_cov100\t6188\t6190\t92.592593\n", "scaffold7_cov100\t6198\t6200\t94.339623\n", "scaffold7_cov100\t7696\t7698\t91.304348\n", "scaffold7_cov100\t7891\t7893\t92.857143\n", "scaffold7_cov100\t8323\t8325\t100.000000\n", "scaffold7_cov100\t9715\t9717\t55.555556\n", "scaffold7_cov100\t9877\t9879\t93.333333\n", "scaffold7_cov100\t10216\t10218\t97.058824\n", "scaffold7_cov100\t10273\t10275\t100.000000\n", "\n", "==> Meth9_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-paCDS <==\n", "scaffold7_cov100\t1390\t1392\t16.666667\n", "scaffold7_cov100\t1941\t1943\t12.500000\n", "scaffold7_cov100\t2043\t2045\t11.111111\n", "scaffold7_cov100\t4630\t4632\t25.000000\n", "scaffold7_cov100\t4678\t4680\t33.333333\n", "scaffold7_cov100\t10755\t10757\t15.000000\n", "scaffold7_cov100\t14042\t14044\t34.615385\n", "scaffold7_cov100\t16387\t16389\t11.111111\n", "scaffold7_cov100\t17952\t17954\t41.463415\n", "scaffold7_cov100\t20473\t20475\t45.945946\n", "\n", "==> Meth9_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-paCDS <==\n", "scaffold6_cov64\t826\t828\t0.000000\n", "scaffold6_cov64\t2097\t2099\t0.000000\n", "scaffold6_cov64\t2179\t2181\t0.000000\n", "scaffold6_cov64\t4793\t4795\t0.000000\n", "scaffold6_cov64\t5581\t5583\t0.000000\n", "scaffold6_cov64\t5583\t5585\t0.000000\n", "scaffold6_cov64\t5592\t5594\t0.000000\n", "scaffold6_cov64\t5594\t5596\t0.000000\n", "scaffold6_cov64\t5604\t5606\t0.000000\n", "scaffold6_cov64\t5644\t5646\t6.250000\n", "\n", "==> Meth9_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-paCDS <==\n", "scaffold6_cov64\t826\t828\t0.000000\n", "scaffold6_cov64\t2097\t2099\t0.000000\n", "scaffold6_cov64\t2179\t2181\t0.000000\n", "scaffold6_cov64\t4793\t4795\t0.000000\n", "scaffold6_cov64\t5581\t5583\t0.000000\n", "scaffold6_cov64\t5583\t5585\t0.000000\n", "scaffold6_cov64\t5592\t5594\t0.000000\n", "scaffold6_cov64\t5594\t5596\t0.000000\n", "scaffold6_cov64\t5604\t5606\t0.000000\n", "scaffold6_cov64\t5644\t5646\t6.250000\n" ] } ], "source": [ "#Check output\n", "!head *paCDS" ] }, { "cell_type": "code", "execution_count": 197, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ " 44391 Meth1_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-paCDS\n", " 69732 Meth1_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-paCDS\n", " 1033482 Meth1_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-paCDS\n", " 1147605 Meth1_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-paCDS\n", " 49447 Meth2_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-paCDS\n", " 59475 Meth2_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-paCDS\n", " 1136063 Meth2_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-paCDS\n", " 1244985 Meth2_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-paCDS\n", " 48847 Meth3_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-paCDS\n", " 69708 Meth3_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-paCDS\n", " 1073682 Meth3_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-paCDS\n", " 1192237 Meth3_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-paCDS\n", " 7459 Meth4_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-paCDS\n", " 28514 Meth4_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-paCDS\n", " 351237 Meth4_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-paCDS\n", " 387210 Meth4_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-paCDS\n", " 6762 Meth5_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-paCDS\n", " 13559 Meth5_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-paCDS\n", " 287611 Meth5_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-paCDS\n", " 307932 Meth5_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-paCDS\n", " 6215 Meth6_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-paCDS\n", " 18448 Meth6_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-paCDS\n", " 297495 Meth6_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-paCDS\n", " 322158 Meth6_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-paCDS\n", " 71918 Meth7_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-paCDS\n", " 69371 Meth7_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-paCDS\n", " 577821 Meth7_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-paCDS\n", " 719110 Meth7_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-paCDS\n", " 55825 Meth8_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-paCDS\n", " 18190 Meth8_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-paCDS\n", " 72799 Meth8_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-paCDS\n", " 146814 Meth8_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-paCDS\n", " 73677 Meth9_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-paCDS\n", " 77848 Meth9_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-paCDS\n", " 560861 Meth9_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-paCDS\n", " 712386 Meth9_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-paCDS\n", " 12360874 total\n" ] } ], "source": [ "#Count number of overlaps\n", "!wc -l *paCDS" ] }, { "cell_type": "code", "execution_count": 198, "metadata": { "collapsed": true }, "outputs": [], "source": [ "!wc -l *paCDS > Pact-5x-paCDS-counts.txt" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "#### 4d. Introns" ] }, { "cell_type": "code", "execution_count": 199, "metadata": { "collapsed": true, "scrolled": true }, "outputs": [], "source": [ "%%bash\n", "\n", "for f in *bed\n", "do\n", " /usr/local/bin/intersectBed \\\n", " -u \\\n", " -a ${f} \\\n", " -b ../../../genome-feature-files/Pact.GFFannotation.Intron.gff \\\n", " > ${f}-paIntron\n", "done" ] }, { "cell_type": "code", "execution_count": 200, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "==> Meth1_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-paIntron <==\n", "scaffold7_cov100\t4351\t4353\t50.000000\n", "scaffold7_cov100\t5578\t5580\t57.142857\n", "scaffold7_cov100\t5986\t5988\t100.000000\n", "scaffold7_cov100\t7438\t7440\t100.000000\n", "scaffold7_cov100\t7796\t7798\t100.000000\n", "scaffold7_cov100\t7891\t7893\t100.000000\n", "scaffold7_cov100\t10414\t10416\t100.000000\n", "scaffold7_cov100\t13385\t13387\t87.500000\n", "scaffold7_cov100\t18941\t18943\t75.000000\n", "scaffold7_cov100\t19095\t19097\t100.000000\n", "\n", "==> Meth1_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-paIntron <==\n", "scaffold7_cov100\t3713\t3715\t16.666667\n", "scaffold7_cov100\t3870\t3872\t11.111111\n", "scaffold7_cov100\t4481\t4483\t20.000000\n", "scaffold7_cov100\t4596\t4598\t12.500000\n", "scaffold7_cov100\t11439\t11441\t44.444444\n", "scaffold7_cov100\t13441\t13443\t20.000000\n", "scaffold7_cov100\t13450\t13452\t40.000000\n", "scaffold7_cov100\t22257\t22259\t33.333333\n", "scaffold7_cov100\t23298\t23300\t40.000000\n", "scaffold7_cov100\t32775\t32777\t16.666667\n", "\n", "==> Meth1_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-paIntron <==\n", "scaffold6_cov64\t167\t169\t0.000000\n", "scaffold6_cov64\t290\t292\t0.000000\n", "scaffold6_cov64\t298\t300\t0.000000\n", "scaffold6_cov64\t489\t491\t0.000000\n", "scaffold6_cov64\t1725\t1727\t0.000000\n", "scaffold6_cov64\t2386\t2388\t0.000000\n", "scaffold6_cov64\t2676\t2678\t0.000000\n", "scaffold6_cov64\t2682\t2684\t0.000000\n", "scaffold6_cov64\t2805\t2807\t5.263158\n", "scaffold6_cov64\t2872\t2874\t0.000000\n", "\n", "==> Meth1_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-paIntron <==\n", "scaffold6_cov64\t167\t169\t0.000000\n", "scaffold6_cov64\t290\t292\t0.000000\n", "scaffold6_cov64\t298\t300\t0.000000\n", "scaffold6_cov64\t489\t491\t0.000000\n", "scaffold6_cov64\t1725\t1727\t0.000000\n", "scaffold6_cov64\t2386\t2388\t0.000000\n", "scaffold6_cov64\t2676\t2678\t0.000000\n", "scaffold6_cov64\t2682\t2684\t0.000000\n", "scaffold6_cov64\t2805\t2807\t5.263158\n", "scaffold6_cov64\t2872\t2874\t0.000000\n", "\n", "==> Meth2_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-paIntron <==\n", "scaffold7_cov100\t5986\t5988\t66.666667\n", "scaffold7_cov100\t7438\t7440\t88.235294\n", "scaffold7_cov100\t7796\t7798\t60.000000\n", "scaffold7_cov100\t7891\t7893\t96.153846\n", "scaffold7_cov100\t10414\t10416\t75.000000\n", "scaffold7_cov100\t13450\t13452\t83.333333\n", "scaffold7_cov100\t19095\t19097\t75.000000\n", "scaffold7_cov100\t20228\t20230\t100.000000\n", "scaffold7_cov100\t20243\t20245\t92.307692\n", "scaffold7_cov100\t20259\t20261\t93.333333\n", "\n", "==> Meth2_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-paIntron <==\n", "scaffold6_cov64\t3978\t3980\t11.111111\n", "scaffold7_cov100\t3994\t3996\t10.526316\n", "scaffold7_cov100\t7121\t7123\t25.000000\n", "scaffold7_cov100\t7201\t7203\t16.666667\n", "scaffold7_cov100\t11439\t11441\t40.000000\n", "scaffold7_cov100\t13385\t13387\t18.750000\n", "scaffold7_cov100\t15312\t15314\t16.666667\n", "scaffold7_cov100\t22257\t22259\t44.444444\n", "scaffold7_cov100\t23298\t23300\t42.857143\n", "scaffold7_cov100\t32007\t32009\t11.111111\n", "\n", "==> Meth2_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-paIntron <==\n", "scaffold6_cov64\t167\t169\t0.000000\n", "scaffold6_cov64\t290\t292\t5.000000\n", "scaffold6_cov64\t298\t300\t0.000000\n", "scaffold6_cov64\t489\t491\t0.000000\n", "scaffold6_cov64\t1725\t1727\t0.000000\n", "scaffold6_cov64\t2386\t2388\t0.000000\n", "scaffold6_cov64\t2440\t2442\t0.000000\n", "scaffold6_cov64\t2488\t2490\t0.000000\n", "scaffold6_cov64\t2536\t2538\t0.000000\n", "scaffold6_cov64\t2584\t2586\t0.000000\n", "\n", "==> Meth2_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-paIntron <==\n", "scaffold6_cov64\t167\t169\t0.000000\n", "scaffold6_cov64\t290\t292\t5.000000\n", "scaffold6_cov64\t298\t300\t0.000000\n", "scaffold6_cov64\t489\t491\t0.000000\n", "scaffold6_cov64\t1725\t1727\t0.000000\n", "scaffold6_cov64\t2386\t2388\t0.000000\n", "scaffold6_cov64\t2440\t2442\t0.000000\n", "scaffold6_cov64\t2488\t2490\t0.000000\n", "scaffold6_cov64\t2536\t2538\t0.000000\n", "scaffold6_cov64\t2584\t2586\t0.000000\n", "\n", "==> Meth3_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-paIntron <==\n", "scaffold7_cov100\t5578\t5580\t55.555556\n", "scaffold7_cov100\t5986\t5988\t60.000000\n", "scaffold7_cov100\t7438\t7440\t100.000000\n", "scaffold7_cov100\t7796\t7798\t81.818182\n", "scaffold7_cov100\t7891\t7893\t100.000000\n", "scaffold7_cov100\t10414\t10416\t100.000000\n", "scaffold7_cov100\t13385\t13387\t92.857143\n", "scaffold7_cov100\t18941\t18943\t72.727273\n", "scaffold7_cov100\t19095\t19097\t100.000000\n", "scaffold7_cov100\t20228\t20230\t100.000000\n", "\n", "==> Meth3_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-paIntron <==\n", "scaffold6_cov64\t1725\t1727\t11.111111\n", "scaffold6_cov64\t3533\t3535\t14.285714\n", "scaffold6_cov64\t5904\t5906\t12.500000\n", "scaffold7_cov100\t4305\t4307\t33.333333\n", "scaffold7_cov100\t4351\t4353\t14.285714\n", "scaffold7_cov100\t7121\t7123\t12.500000\n", "scaffold7_cov100\t7201\t7203\t42.857143\n", "scaffold7_cov100\t11439\t11441\t41.666667\n", "scaffold7_cov100\t13450\t13452\t27.272727\n", "scaffold7_cov100\t22257\t22259\t22.222222\n", "\n", "==> Meth3_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-paIntron <==\n", "scaffold6_cov64\t167\t169\t0.000000\n", "scaffold6_cov64\t290\t292\t0.000000\n", "scaffold6_cov64\t298\t300\t0.000000\n", "scaffold6_cov64\t489\t491\t0.000000\n", "scaffold6_cov64\t2386\t2388\t0.000000\n", "scaffold6_cov64\t2676\t2678\t0.000000\n", "scaffold6_cov64\t2682\t2684\t0.000000\n", "scaffold6_cov64\t2805\t2807\t0.000000\n", "scaffold6_cov64\t2872\t2874\t0.000000\n", "scaffold6_cov64\t2876\t2878\t0.000000\n", "\n", "==> Meth3_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-paIntron <==\n", "scaffold6_cov64\t167\t169\t0.000000\n", "scaffold6_cov64\t290\t292\t0.000000\n", "scaffold6_cov64\t298\t300\t0.000000\n", "scaffold6_cov64\t489\t491\t0.000000\n", "scaffold6_cov64\t1725\t1727\t11.111111\n", "scaffold6_cov64\t2386\t2388\t0.000000\n", "scaffold6_cov64\t2676\t2678\t0.000000\n", "scaffold6_cov64\t2682\t2684\t0.000000\n", "scaffold6_cov64\t2805\t2807\t0.000000\n", "scaffold6_cov64\t2872\t2874\t0.000000\n", "\n", "==> Meth4_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-paIntron <==\n", "scaffold7_cov100\t109716\t109718\t60.000000\n", "scaffold7_cov100\t201089\t201091\t60.000000\n", "scaffold7_cov100\t201104\t201106\t60.000000\n", "scaffold7_cov100\t201111\t201113\t60.000000\n", "scaffold7_cov100\t201124\t201126\t60.000000\n", "scaffold7_cov100\t202376\t202378\t88.888889\n", "scaffold7_cov100\t213076\t213078\t60.000000\n", "scaffold7_cov100\t213138\t213140\t60.000000\n", "scaffold7_cov100\t393508\t393510\t83.333333\n", "scaffold7_cov100\t393563\t393565\t100.000000\n", "\n", "==> Meth4_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-paIntron <==\n", "scaffold6_cov64\t2676\t2678\t20.000000\n", "scaffold6_cov64\t5904\t5906\t15.485564\n", "scaffold7_cov100\t4351\t4353\t46.428571\n", "scaffold7_cov100\t46898\t46900\t20.000000\n", "scaffold7_cov100\t55614\t55616\t11.111111\n", "scaffold7_cov100\t81500\t81502\t16.666667\n", "scaffold7_cov100\t90556\t90558\t28.571429\n", "scaffold7_cov100\t91941\t91943\t20.000000\n", "scaffold7_cov100\t109714\t109716\t25.000000\n", "scaffold7_cov100\t109873\t109875\t33.333333\n", "\n", "==> Meth4_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-paIntron <==\n", "scaffold6_cov64\t2536\t2538\t0.000000\n", "scaffold6_cov64\t2584\t2586\t0.000000\n", "scaffold6_cov64\t4588\t4590\t0.000000\n", "scaffold6_cov64\t5101\t5103\t0.000000\n", "scaffold6_cov64\t5309\t5311\t0.000000\n", "scaffold6_cov64\t5456\t5458\t0.000000\n", "scaffold6_cov64\t5486\t5488\t0.000000\n", "scaffold6_cov64\t5545\t5547\t0.000000\n", "scaffold6_cov64\t5559\t5561\t0.000000\n", "scaffold6_cov64\t5561\t5563\t2.941176\n", "\n", "==> Meth4_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-paIntron <==\n", "scaffold6_cov64\t2536\t2538\t0.000000\n", "scaffold6_cov64\t2584\t2586\t0.000000\n", "scaffold6_cov64\t2676\t2678\t20.000000\n", "scaffold6_cov64\t4588\t4590\t0.000000\n", "scaffold6_cov64\t5101\t5103\t0.000000\n", "scaffold6_cov64\t5309\t5311\t0.000000\n", "scaffold6_cov64\t5456\t5458\t0.000000\n", "scaffold6_cov64\t5486\t5488\t0.000000\n", "scaffold6_cov64\t5545\t5547\t0.000000\n", "scaffold6_cov64\t5559\t5561\t0.000000\n", "\n", "==> Meth5_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-paIntron <==\n", "scaffold6_cov64\t2676\t2678\t77.777778\n", "scaffold7_cov100\t96721\t96723\t83.333333\n", "scaffold7_cov100\t96740\t96742\t71.428571\n", "scaffold7_cov100\t177834\t177836\t50.000000\n", "scaffold7_cov100\t177838\t177840\t65.517241\n", "scaffold7_cov100\t253591\t253593\t71.428571\n", "scaffold7_cov100\t394699\t394701\t97.297297\n", "scaffold7_cov100\t483848\t483850\t50.000000\n", "scaffold7_cov100\t496950\t496952\t100.000000\n", "scaffold12_cov67\t4517\t4519\t50.000000\n", "\n", "==> Meth5_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-paIntron <==\n", "scaffold6_cov64\t4553\t4555\t20.000000\n", "scaffold6_cov64\t5545\t5547\t14.285714\n", "scaffold6_cov64\t6374\t6376\t45.454545\n", "scaffold7_cov100\t36543\t36545\t25.000000\n", "scaffold7_cov100\t36600\t36602\t25.000000\n", "scaffold7_cov100\t120495\t120497\t40.000000\n", "scaffold7_cov100\t157191\t157193\t20.000000\n", "scaffold7_cov100\t158929\t158931\t33.333333\n", "scaffold7_cov100\t177836\t177838\t22.222222\n", "scaffold7_cov100\t205953\t205955\t42.857143\n", "\n", "==> Meth5_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-paIntron <==\n", "scaffold6_cov64\t2584\t2586\t0.000000\n", "scaffold6_cov64\t2682\t2684\t0.000000\n", "scaffold6_cov64\t4588\t4590\t0.000000\n", "scaffold6_cov64\t5559\t5561\t7.692308\n", "scaffold6_cov64\t5561\t5563\t7.142857\n", "scaffold6_cov64\t5567\t5569\t0.000000\n", "scaffold6_cov64\t5574\t5576\t5.263158\n", "scaffold6_cov64\t5581\t5583\t0.000000\n", "scaffold6_cov64\t5583\t5585\t0.000000\n", "scaffold6_cov64\t5592\t5594\t0.000000\n", "\n", "==> Meth5_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-paIntron <==\n", "scaffold6_cov64\t2584\t2586\t0.000000\n", "scaffold6_cov64\t2676\t2678\t77.777778\n", "scaffold6_cov64\t2682\t2684\t0.000000\n", "scaffold6_cov64\t4553\t4555\t20.000000\n", "scaffold6_cov64\t4588\t4590\t0.000000\n", "scaffold6_cov64\t5545\t5547\t14.285714\n", "scaffold6_cov64\t5559\t5561\t7.692308\n", "scaffold6_cov64\t5561\t5563\t7.142857\n", "scaffold6_cov64\t5567\t5569\t0.000000\n", "scaffold6_cov64\t5574\t5576\t5.263158\n", "\n", "==> Meth6_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-paIntron <==\n", "scaffold7_cov100\t394699\t394701\t95.555556\n", "scaffold12_cov67\t4363\t4365\t50.000000\n", "scaffold12_cov67\t4517\t4519\t50.000000\n", "scaffold12_cov67\t11660\t11662\t73.913043\n", "scaffold19_cov103\t69462\t69464\t70.000000\n", "scaffold22_cov58\t5787\t5789\t83.333333\n", "scaffold27_cov99\t17698\t17700\t62.500000\n", "scaffold27_cov99\t98212\t98214\t50.000000\n", "scaffold28_cov97\t88105\t88107\t66.666667\n", "scaffold28_cov97\t97312\t97314\t71.428571\n", "\n", "==> Meth6_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-paIntron <==\n", "scaffold6_cov64\t4553\t4555\t14.285714\n", "scaffold6_cov64\t4588\t4590\t22.222222\n", "scaffold6_cov64\t6266\t6268\t14.285714\n", "scaffold6_cov64\t6374\t6376\t20.000000\n", "scaffold7_cov100\t4351\t4353\t10.256410\n", "scaffold7_cov100\t32521\t32523\t18.750000\n", "scaffold7_cov100\t37484\t37486\t16.666667\n", "scaffold7_cov100\t37506\t37508\t16.666667\n", "scaffold7_cov100\t37534\t37536\t16.666667\n", "scaffold7_cov100\t47010\t47012\t33.333333\n", "\n", "==> Meth6_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-paIntron <==\n", "scaffold6_cov64\t5456\t5458\t0.000000\n", "scaffold6_cov64\t5486\t5488\t0.000000\n", "scaffold6_cov64\t5545\t5547\t0.000000\n", "scaffold6_cov64\t5559\t5561\t4.166667\n", "scaffold6_cov64\t5561\t5563\t0.000000\n", "scaffold6_cov64\t5567\t5569\t0.000000\n", "scaffold6_cov64\t5574\t5576\t0.000000\n", "scaffold6_cov64\t5581\t5583\t8.333333\n", "scaffold6_cov64\t5583\t5585\t0.000000\n", "scaffold6_cov64\t5592\t5594\t0.000000\n", "\n", "==> Meth6_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-paIntron <==\n", "scaffold6_cov64\t4553\t4555\t14.285714\n", "scaffold6_cov64\t4588\t4590\t22.222222\n", "scaffold6_cov64\t5456\t5458\t0.000000\n", "scaffold6_cov64\t5486\t5488\t0.000000\n", "scaffold6_cov64\t5545\t5547\t0.000000\n", "scaffold6_cov64\t5559\t5561\t4.166667\n", "scaffold6_cov64\t5561\t5563\t0.000000\n", "scaffold6_cov64\t5567\t5569\t0.000000\n", "scaffold6_cov64\t5574\t5576\t0.000000\n", "scaffold6_cov64\t5581\t5583\t8.333333\n", "\n", "==> Meth7_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-paIntron <==\n", "scaffold7_cov100\t5986\t5988\t73.333333\n", "scaffold7_cov100\t7438\t7440\t100.000000\n", "scaffold7_cov100\t7796\t7798\t95.454545\n", "scaffold7_cov100\t7891\t7893\t100.000000\n", "scaffold7_cov100\t10414\t10416\t94.117647\n", "scaffold7_cov100\t13385\t13387\t86.842105\n", "scaffold7_cov100\t13450\t13452\t61.538462\n", "scaffold7_cov100\t18941\t18943\t68.085106\n", "scaffold7_cov100\t19095\t19097\t83.333333\n", "scaffold7_cov100\t20228\t20230\t95.454545\n", "\n", "==> Meth7_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-paIntron <==\n", "scaffold6_cov64\t4146\t4148\t20.000000\n", "scaffold6_cov64\t5561\t5563\t14.285714\n", "scaffold7_cov100\t3629\t3631\t12.500000\n", "scaffold7_cov100\t5578\t5580\t42.857143\n", "scaffold7_cov100\t11439\t11441\t25.000000\n", "scaffold7_cov100\t36904\t36906\t14.285714\n", "scaffold7_cov100\t36971\t36973\t16.666667\n", "scaffold7_cov100\t46983\t46985\t12.500000\n", "scaffold7_cov100\t52640\t52642\t28.571429\n", "scaffold7_cov100\t52903\t52905\t36.363636\n", "\n", "==> Meth7_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-paIntron <==\n", "scaffold6_cov64\t290\t292\t0.000000\n", "scaffold6_cov64\t298\t300\t0.000000\n", "scaffold6_cov64\t489\t491\t0.000000\n", "scaffold6_cov64\t2872\t2874\t0.000000\n", "scaffold6_cov64\t2876\t2878\t0.000000\n", "scaffold6_cov64\t3198\t3200\t0.000000\n", "scaffold6_cov64\t3343\t3345\t0.000000\n", "scaffold6_cov64\t3397\t3399\t0.000000\n", "scaffold6_cov64\t3412\t3414\t0.000000\n", "scaffold6_cov64\t3420\t3422\t10.000000\n", "\n", "==> Meth7_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-paIntron <==\n", "scaffold6_cov64\t290\t292\t0.000000\n", "scaffold6_cov64\t298\t300\t0.000000\n", "scaffold6_cov64\t489\t491\t0.000000\n", "scaffold6_cov64\t2872\t2874\t0.000000\n", "scaffold6_cov64\t2876\t2878\t0.000000\n", "scaffold6_cov64\t3198\t3200\t0.000000\n", "scaffold6_cov64\t3343\t3345\t0.000000\n", "scaffold6_cov64\t3397\t3399\t0.000000\n", "scaffold6_cov64\t3412\t3414\t0.000000\n", "scaffold6_cov64\t3420\t3422\t10.000000\n", "\n", "==> Meth8_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-paIntron <==\n", "scaffold7_cov100\t5986\t5988\t78.947368\n", "scaffold7_cov100\t7796\t7798\t72.727273\n", "scaffold7_cov100\t7891\t7893\t90.000000\n", "scaffold7_cov100\t19095\t19097\t90.909091\n", "scaffold7_cov100\t20228\t20230\t96.666667\n", "scaffold7_cov100\t20243\t20245\t96.875000\n", "scaffold7_cov100\t20259\t20261\t100.000000\n", "scaffold7_cov100\t53052\t53054\t76.923077\n", "scaffold7_cov100\t77503\t77505\t54.545455\n", "scaffold7_cov100\t114325\t114327\t82.051282\n", "\n", "==> Meth8_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-paIntron <==\n", "scaffold7_cov100\t7438\t7440\t40.000000\n", "scaffold7_cov100\t13385\t13387\t46.666667\n", "scaffold7_cov100\t22257\t22259\t20.000000\n", "scaffold7_cov100\t34847\t34849\t20.000000\n", "scaffold7_cov100\t52903\t52905\t33.333333\n", "scaffold7_cov100\t69268\t69270\t40.000000\n", "scaffold7_cov100\t119845\t119847\t20.000000\n", "scaffold7_cov100\t155682\t155684\t15.686275\n", "scaffold7_cov100\t349037\t349039\t16.666667\n", "scaffold7_cov100\t459144\t459146\t20.000000\n", "\n", "==> Meth8_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-paIntron <==\n", "scaffold6_cov64\t290\t292\t0.000000\n", "scaffold6_cov64\t298\t300\t0.000000\n", "scaffold6_cov64\t5101\t5103\t0.000000\n", "scaffold6_cov64\t5545\t5547\t0.000000\n", "scaffold6_cov64\t5559\t5561\t0.000000\n", "scaffold6_cov64\t5561\t5563\t0.000000\n", "scaffold6_cov64\t5567\t5569\t0.000000\n", "scaffold6_cov64\t5574\t5576\t0.000000\n", "scaffold6_cov64\t5581\t5583\t0.000000\n", "scaffold6_cov64\t6266\t6268\t0.000000\n", "\n", "==> Meth8_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-paIntron <==\n", "scaffold6_cov64\t290\t292\t0.000000\n", "scaffold6_cov64\t298\t300\t0.000000\n", "scaffold6_cov64\t5101\t5103\t0.000000\n", "scaffold6_cov64\t5545\t5547\t0.000000\n", "scaffold6_cov64\t5559\t5561\t0.000000\n", "scaffold6_cov64\t5561\t5563\t0.000000\n", "scaffold6_cov64\t5567\t5569\t0.000000\n", "scaffold6_cov64\t5574\t5576\t0.000000\n", "scaffold6_cov64\t5581\t5583\t0.000000\n", "scaffold6_cov64\t6266\t6268\t0.000000\n", "\n", "==> Meth9_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-paIntron <==\n", "scaffold7_cov100\t5578\t5580\t66.666667\n", "scaffold7_cov100\t5986\t5988\t79.166667\n", "scaffold7_cov100\t7201\t7203\t80.000000\n", "scaffold7_cov100\t7438\t7440\t100.000000\n", "scaffold7_cov100\t7796\t7798\t100.000000\n", "scaffold7_cov100\t7891\t7893\t92.857143\n", "scaffold7_cov100\t10414\t10416\t92.857143\n", "scaffold7_cov100\t11439\t11441\t60.000000\n", "scaffold7_cov100\t13385\t13387\t88.461538\n", "scaffold7_cov100\t13450\t13452\t58.823529\n", "\n", "==> Meth9_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-paIntron <==\n", "scaffold6_cov64\t3435\t3437\t15.384615\n", "scaffold6_cov64\t4146\t4148\t12.500000\n", "scaffold6_cov64\t5904\t5906\t14.285714\n", "scaffold7_cov100\t3956\t3958\t20.000000\n", "scaffold7_cov100\t35655\t35657\t33.333333\n", "scaffold7_cov100\t35661\t35663\t14.285714\n", "scaffold7_cov100\t36634\t36636\t16.666667\n", "scaffold7_cov100\t43825\t43827\t16.666667\n", "scaffold7_cov100\t43840\t43842\t40.000000\n", "scaffold7_cov100\t43874\t43876\t16.666667\n", "\n", "==> Meth9_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-paIntron <==\n", "scaffold6_cov64\t290\t292\t0.000000\n", "scaffold6_cov64\t298\t300\t0.000000\n", "scaffold6_cov64\t489\t491\t0.000000\n", "scaffold6_cov64\t2805\t2807\t0.000000\n", "scaffold6_cov64\t3198\t3200\t0.000000\n", "scaffold6_cov64\t3343\t3345\t0.000000\n", "scaffold6_cov64\t3397\t3399\t0.000000\n", "scaffold6_cov64\t3412\t3414\t0.000000\n", "scaffold6_cov64\t3420\t3422\t0.000000\n", "scaffold6_cov64\t3439\t3441\t7.692308\n", "\n", "==> Meth9_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-paIntron <==\n", "scaffold6_cov64\t290\t292\t0.000000\n", "scaffold6_cov64\t298\t300\t0.000000\n", "scaffold6_cov64\t489\t491\t0.000000\n", "scaffold6_cov64\t2805\t2807\t0.000000\n", "scaffold6_cov64\t3198\t3200\t0.000000\n", "scaffold6_cov64\t3343\t3345\t0.000000\n", "scaffold6_cov64\t3397\t3399\t0.000000\n", "scaffold6_cov64\t3412\t3414\t0.000000\n", "scaffold6_cov64\t3420\t3422\t0.000000\n", "scaffold6_cov64\t3435\t3437\t15.384615\n" ] } ], "source": [ "#Check output\n", "!head *paIntron" ] }, { "cell_type": "code", "execution_count": 201, "metadata": { "collapsed": false, "scrolled": true }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ " 30313 Meth1_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-paIntron\n", " 88506 Meth1_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-paIntron\n", " 1212927 Meth1_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-paIntron\n", " 1331746 Meth1_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-paIntron\n", " 37312 Meth2_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-paIntron\n", " 85627 Meth2_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-paIntron\n", " 1407919 Meth2_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-paIntron\n", " 1530858 Meth2_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-paIntron\n", " 34362 Meth3_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-paIntron\n", " 92942 Meth3_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-paIntron\n", " 1281701 Meth3_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-paIntron\n", " 1409005 Meth3_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-paIntron\n", " 6201 Meth4_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-paIntron\n", " 28028 Meth4_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-paIntron\n", " 358170 Meth4_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-paIntron\n", " 392399 Meth4_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-paIntron\n", " 6083 Meth5_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-paIntron\n", " 12520 Meth5_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-paIntron\n", " 283366 Meth5_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-paIntron\n", " 301969 Meth5_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-paIntron\n", " 5235 Meth6_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-paIntron\n", " 17325 Meth6_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-paIntron\n", " 297640 Meth6_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-paIntron\n", " 320200 Meth6_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-paIntron\n", " 47394 Meth7_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-paIntron\n", " 51739 Meth7_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-paIntron\n", " 441740 Meth7_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-paIntron\n", " 540873 Meth7_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-paIntron\n", " 30922 Meth8_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-paIntron\n", " 9882 Meth8_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-paIntron\n", " 33695 Meth8_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-paIntron\n", " 74499 Meth8_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-paIntron\n", " 52983 Meth9_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-paIntron\n", " 61846 Meth9_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-paIntron\n", " 460776 Meth9_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-paIntron\n", " 575605 Meth9_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-paIntron\n", " 12954308 total\n" ] } ], "source": [ "#Count number of overlaps\n", "!wc -l *paIntron" ] }, { "cell_type": "code", "execution_count": 202, "metadata": { "collapsed": true }, "outputs": [], "source": [ "!wc -l *paIntron > Pact-5x-paIntron-counts.txt" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "#### 4e. Flanking regions" ] }, { "cell_type": "code", "execution_count": 203, "metadata": { "collapsed": true, "scrolled": true }, "outputs": [], "source": [ "%%bash\n", "\n", "for f in *bed\n", "do\n", " /usr/local/bin/intersectBed \\\n", " -u \\\n", " -a ${f} \\\n", " -b ../../../genome-feature-files/Pact.GFFannotation.flanks.gff \\\n", " > ${f}-paFlanks\n", "done" ] }, { "cell_type": "code", "execution_count": 204, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "==> Meth1_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-paFlanks <==\r\n", "scaffold7_cov100\t6231\t6233\t100.000000\r\n", "scaffold7_cov100\t6233\t6235\t100.000000\r\n", "scaffold7_cov100\t19284\t19286\t85.714286\r\n", "scaffold7_cov100\t19296\t19298\t100.000000\r\n", "scaffold7_cov100\t24494\t24496\t60.000000\r\n", "scaffold7_cov100\t24509\t24511\t88.888889\r\n", "scaffold7_cov100\t24557\t24559\t50.000000\r\n", "scaffold7_cov100\t24617\t24619\t66.666667\r\n", "scaffold7_cov100\t24895\t24897\t85.714286\r\n", "scaffold7_cov100\t24941\t24943\t72.727273\r\n", "\r\n", "==> Meth1_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-paFlanks <==\r\n", "scaffold6_cov64\t7373\t7375\t12.500000\r\n", "scaffold7_cov100\t13275\t13277\t40.000000\r\n", "scaffold7_cov100\t15597\t15599\t33.333333\r\n", "scaffold7_cov100\t24454\t24456\t36.363636\r\n", "scaffold7_cov100\t24614\t24616\t22.222222\r\n", "scaffold7_cov100\t24769\t24771\t40.000000\r\n", "scaffold7_cov100\t24830\t24832\t28.571429\r\n", "scaffold7_cov100\t25157\t25159\t16.666667\r\n", "scaffold7_cov100\t28495\t28497\t12.500000\r\n", "scaffold7_cov100\t30593\t30595\t11.111111\r\n", "\r\n", "==> Meth1_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-paFlanks <==\r\n", "scaffold6_cov64\t5797\t5799\t3.125000\r\n", "scaffold6_cov64\t5800\t5802\t3.030303\r\n", "scaffold6_cov64\t6704\t6706\t0.000000\r\n", "scaffold6_cov64\t6751\t6753\t0.000000\r\n", "scaffold6_cov64\t6805\t6807\t0.000000\r\n", "scaffold6_cov64\t6813\t6815\t0.000000\r\n", "scaffold6_cov64\t6862\t6864\t0.000000\r\n", "scaffold6_cov64\t6880\t6882\t0.000000\r\n", "scaffold6_cov64\t6885\t6887\t0.000000\r\n", "scaffold6_cov64\t6909\t6911\t0.000000\r\n", "\r\n", "==> Meth1_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-paFlanks <==\r\n", "scaffold6_cov64\t5797\t5799\t3.125000\r\n", "scaffold6_cov64\t5800\t5802\t3.030303\r\n", "scaffold6_cov64\t6704\t6706\t0.000000\r\n", "scaffold6_cov64\t6751\t6753\t0.000000\r\n", "scaffold6_cov64\t6805\t6807\t0.000000\r\n", "scaffold6_cov64\t6813\t6815\t0.000000\r\n", "scaffold6_cov64\t6862\t6864\t0.000000\r\n", "scaffold6_cov64\t6880\t6882\t0.000000\r\n", "scaffold6_cov64\t6885\t6887\t0.000000\r\n", "scaffold6_cov64\t6909\t6911\t0.000000\r\n", "\r\n", "==> Meth2_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-paFlanks <==\r\n", "scaffold7_cov100\t6231\t6233\t71.428571\r\n", "scaffold7_cov100\t6233\t6235\t100.000000\r\n", "scaffold7_cov100\t11815\t11817\t77.777778\r\n", "scaffold7_cov100\t12247\t12249\t54.545455\r\n", "scaffold7_cov100\t13275\t13277\t100.000000\r\n", "scaffold7_cov100\t19284\t19286\t92.307692\r\n", "scaffold7_cov100\t19296\t19298\t92.857143\r\n", "scaffold7_cov100\t24401\t24403\t100.000000\r\n", "scaffold7_cov100\t24443\t24445\t66.666667\r\n", "scaffold7_cov100\t24454\t24456\t100.000000\r\n", "\r\n", "==> Meth2_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-paFlanks <==\r\n", "scaffold6_cov64\t7077\t7079\t12.500000\r\n", "scaffold7_cov100\t2652\t2654\t16.666667\r\n", "scaffold7_cov100\t12131\t12133\t28.571429\r\n", "scaffold7_cov100\t18520\t18522\t20.000000\r\n", "scaffold7_cov100\t24494\t24496\t28.571429\r\n", "scaffold7_cov100\t24895\t24897\t38.888889\r\n", "scaffold7_cov100\t25157\t25159\t47.058824\r\n", "scaffold7_cov100\t27904\t27906\t20.000000\r\n", "scaffold7_cov100\t27980\t27982\t20.000000\r\n", "scaffold7_cov100\t28393\t28395\t14.285714\r\n", "\r\n", "==> Meth2_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-paFlanks <==\r\n", "scaffold6_cov64\t5797\t5799\t0.000000\r\n", "scaffold6_cov64\t5800\t5802\t0.000000\r\n", "scaffold6_cov64\t6690\t6692\t0.000000\r\n", "scaffold6_cov64\t6704\t6706\t0.000000\r\n", "scaffold6_cov64\t6732\t6734\t0.000000\r\n", "scaffold6_cov64\t6751\t6753\t0.000000\r\n", "scaffold6_cov64\t6805\t6807\t0.000000\r\n", "scaffold6_cov64\t6813\t6815\t5.263158\r\n", "scaffold6_cov64\t6862\t6864\t0.000000\r\n", "scaffold6_cov64\t6880\t6882\t0.000000\r\n", "\r\n", "==> Meth2_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-paFlanks <==\r\n", "scaffold6_cov64\t5797\t5799\t0.000000\r\n", "scaffold6_cov64\t5800\t5802\t0.000000\r\n", "scaffold6_cov64\t6690\t6692\t0.000000\r\n", "scaffold6_cov64\t6704\t6706\t0.000000\r\n", "scaffold6_cov64\t6732\t6734\t0.000000\r\n", "scaffold6_cov64\t6751\t6753\t0.000000\r\n", "scaffold6_cov64\t6805\t6807\t0.000000\r\n", "scaffold6_cov64\t6813\t6815\t5.263158\r\n", "scaffold6_cov64\t6862\t6864\t0.000000\r\n", "scaffold6_cov64\t6880\t6882\t0.000000\r\n", "\r\n", "==> Meth3_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-paFlanks <==\r\n", "scaffold7_cov100\t6231\t6233\t100.000000\r\n", "scaffold7_cov100\t6233\t6235\t100.000000\r\n", "scaffold7_cov100\t11815\t11817\t50.000000\r\n", "scaffold7_cov100\t18520\t18522\t66.666667\r\n", "scaffold7_cov100\t19284\t19286\t80.000000\r\n", "scaffold7_cov100\t19296\t19298\t88.888889\r\n", "scaffold7_cov100\t24401\t24403\t100.000000\r\n", "scaffold7_cov100\t24454\t24456\t66.666667\r\n", "scaffold7_cov100\t24509\t24511\t100.000000\r\n", "scaffold7_cov100\t24617\t24619\t61.538462\r\n", "\r\n", "==> Meth3_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-paFlanks <==\r\n", "scaffold6_cov64\t6732\t6734\t14.285714\r\n", "scaffold7_cov100\t2708\t2710\t11.111111\r\n", "scaffold7_cov100\t3297\t3299\t12.500000\r\n", "scaffold7_cov100\t13275\t13277\t22.222222\r\n", "scaffold7_cov100\t24494\t24496\t22.222222\r\n", "scaffold7_cov100\t24557\t24559\t28.571429\r\n", "scaffold7_cov100\t24614\t24616\t23.076923\r\n", "scaffold7_cov100\t24969\t24971\t12.500000\r\n", "scaffold7_cov100\t25157\t25159\t23.529412\r\n", "scaffold7_cov100\t27596\t27598\t14.285714\r\n", "\r\n", "==> Meth3_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-paFlanks <==\r\n", "scaffold6_cov64\t5797\t5799\t0.000000\r\n", "scaffold6_cov64\t5800\t5802\t0.000000\r\n", "scaffold6_cov64\t6690\t6692\t0.000000\r\n", "scaffold6_cov64\t6704\t6706\t0.000000\r\n", "scaffold6_cov64\t6751\t6753\t0.000000\r\n", "scaffold6_cov64\t6805\t6807\t0.000000\r\n", "scaffold6_cov64\t6813\t6815\t3.571429\r\n", "scaffold6_cov64\t6862\t6864\t4.000000\r\n", "scaffold6_cov64\t6880\t6882\t0.000000\r\n", "scaffold6_cov64\t6885\t6887\t0.000000\r\n", "\r\n", "==> Meth3_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-paFlanks <==\r\n", "scaffold6_cov64\t5797\t5799\t0.000000\r\n", "scaffold6_cov64\t5800\t5802\t0.000000\r\n", "scaffold6_cov64\t6690\t6692\t0.000000\r\n", "scaffold6_cov64\t6704\t6706\t0.000000\r\n", "scaffold6_cov64\t6732\t6734\t14.285714\r\n", "scaffold6_cov64\t6751\t6753\t0.000000\r\n", "scaffold6_cov64\t6805\t6807\t0.000000\r\n", "scaffold6_cov64\t6813\t6815\t3.571429\r\n", "scaffold6_cov64\t6862\t6864\t4.000000\r\n", "scaffold6_cov64\t6880\t6882\t0.000000\r\n", "\r\n", "==> Meth4_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-paFlanks <==\r\n", "scaffold7_cov100\t24509\t24511\t100.000000\r\n", "scaffold7_cov100\t24557\t24559\t100.000000\r\n", "scaffold7_cov100\t40896\t40898\t50.000000\r\n", "scaffold7_cov100\t342219\t342221\t50.000000\r\n", "scaffold7_cov100\t384784\t384786\t50.000000\r\n", "scaffold7_cov100\t443190\t443192\t100.000000\r\n", "scaffold7_cov100\t443210\t443212\t100.000000\r\n", "scaffold7_cov100\t450123\t450125\t100.000000\r\n", "scaffold20_cov103\t50562\t50564\t60.000000\r\n", "scaffold20_cov103\t69200\t69202\t100.000000\r\n", "\r\n", "==> Meth4_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-paFlanks <==\r\n", "scaffold6_cov64\t6732\t6734\t16.666667\r\n", "scaffold7_cov100\t38369\t38371\t11.111111\r\n", "scaffold7_cov100\t40816\t40818\t40.000000\r\n", "scaffold7_cov100\t40898\t40900\t16.666667\r\n", "scaffold7_cov100\t40917\t40919\t20.000000\r\n", "scaffold7_cov100\t40936\t40938\t20.000000\r\n", "scaffold7_cov100\t49302\t49304\t42.857143\r\n", "scaffold7_cov100\t49331\t49333\t37.500000\r\n", "scaffold7_cov100\t49341\t49343\t37.500000\r\n", "scaffold7_cov100\t49347\t49349\t33.333333\r\n", "\r\n", "==> Meth4_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-paFlanks <==\r\n", "scaffold6_cov64\t5797\t5799\t0.629811\r\n", "scaffold6_cov64\t5800\t5802\t0.700771\r\n", "scaffold6_cov64\t6687\t6689\t6.666667\r\n", "scaffold6_cov64\t6690\t6692\t0.000000\r\n", "scaffold6_cov64\t6704\t6706\t2.702703\r\n", "scaffold6_cov64\t6751\t6753\t8.000000\r\n", "scaffold6_cov64\t6805\t6807\t0.000000\r\n", "scaffold6_cov64\t6813\t6815\t0.000000\r\n", "scaffold6_cov64\t6862\t6864\t0.000000\r\n", "scaffold6_cov64\t6880\t6882\t0.000000\r\n", "\r\n", "==> Meth4_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-paFlanks <==\r\n", "scaffold6_cov64\t5797\t5799\t0.629811\r\n", "scaffold6_cov64\t5800\t5802\t0.700771\r\n", "scaffold6_cov64\t6687\t6689\t6.666667\r\n", "scaffold6_cov64\t6690\t6692\t0.000000\r\n", "scaffold6_cov64\t6704\t6706\t2.702703\r\n", "scaffold6_cov64\t6732\t6734\t16.666667\r\n", "scaffold6_cov64\t6751\t6753\t8.000000\r\n", "scaffold6_cov64\t6805\t6807\t0.000000\r\n", "scaffold6_cov64\t6813\t6815\t0.000000\r\n", "scaffold6_cov64\t6862\t6864\t0.000000\r\n", "\r\n", "==> Meth5_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-paFlanks <==\r\n", "scaffold7_cov100\t24454\t24456\t100.000000\r\n", "scaffold7_cov100\t24494\t24496\t87.500000\r\n", "scaffold7_cov100\t24509\t24511\t100.000000\r\n", "scaffold7_cov100\t24557\t24559\t100.000000\r\n", "scaffold7_cov100\t92029\t92031\t100.000000\r\n", "scaffold7_cov100\t151631\t151633\t50.000000\r\n", "scaffold7_cov100\t219436\t219438\t57.142857\r\n", "scaffold7_cov100\t281483\t281485\t60.000000\r\n", "scaffold7_cov100\t281501\t281503\t60.000000\r\n", "scaffold7_cov100\t342219\t342221\t88.888889\r\n", "\r\n", "==> Meth5_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-paFlanks <==\r\n", "scaffold7_cov100\t24443\t24445\t16.666667\r\n", "scaffold7_cov100\t91999\t92001\t14.285714\r\n", "scaffold7_cov100\t116515\t116517\t20.000000\r\n", "scaffold7_cov100\t131309\t131311\t11.764706\r\n", "scaffold7_cov100\t162610\t162612\t20.000000\r\n", "scaffold7_cov100\t198799\t198801\t14.285714\r\n", "scaffold7_cov100\t210084\t210086\t22.222222\r\n", "scaffold7_cov100\t218601\t218603\t10.655738\r\n", "scaffold7_cov100\t219440\t219442\t20.000000\r\n", "scaffold7_cov100\t259165\t259167\t16.666667\r\n", "\r\n", "==> Meth5_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-paFlanks <==\r\n", "scaffold6_cov64\t5797\t5799\t0.654664\r\n", "scaffold6_cov64\t5800\t5802\t0.572988\r\n", "scaffold6_cov64\t6687\t6689\t0.000000\r\n", "scaffold6_cov64\t6690\t6692\t0.000000\r\n", "scaffold6_cov64\t6704\t6706\t0.000000\r\n", "scaffold6_cov64\t6751\t6753\t0.000000\r\n", "scaffold6_cov64\t6805\t6807\t0.000000\r\n", "scaffold6_cov64\t6813\t6815\t0.000000\r\n", "scaffold7_cov100\t3150\t3152\t5.004634\r\n", "scaffold7_cov100\t3194\t3196\t0.587988\r\n", "\r\n", "==> Meth5_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-paFlanks <==\r\n", "scaffold6_cov64\t5797\t5799\t0.654664\r\n", "scaffold6_cov64\t5800\t5802\t0.572988\r\n", "scaffold6_cov64\t6687\t6689\t0.000000\r\n", "scaffold6_cov64\t6690\t6692\t0.000000\r\n", "scaffold6_cov64\t6704\t6706\t0.000000\r\n", "scaffold6_cov64\t6751\t6753\t0.000000\r\n", "scaffold6_cov64\t6805\t6807\t0.000000\r\n", "scaffold6_cov64\t6813\t6815\t0.000000\r\n", "scaffold7_cov100\t3150\t3152\t5.004634\r\n", "scaffold7_cov100\t3194\t3196\t0.587988\r\n", "\r\n", "==> Meth6_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-paFlanks <==\r\n", "scaffold7_cov100\t151631\t151633\t60.000000\r\n", "scaffold7_cov100\t210167\t210169\t83.333333\r\n", "scaffold7_cov100\t281483\t281485\t50.000000\r\n", "scaffold7_cov100\t281501\t281503\t55.555556\r\n", "scaffold7_cov100\t443190\t443192\t100.000000\r\n", "scaffold12_cov67\t28089\t28091\t100.000000\r\n", "scaffold19_cov103\t94546\t94548\t50.000000\r\n", "scaffold19_cov103\t148521\t148523\t62.500000\r\n", "scaffold19_cov103\t148544\t148546\t62.500000\r\n", "scaffold19_cov103\t148559\t148561\t62.500000\r\n", "\r\n", "==> Meth6_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-paFlanks <==\r\n", "scaffold6_cov64\t6687\t6689\t14.285714\r\n", "scaffold6_cov64\t6704\t6706\t14.285714\r\n", "scaffold6_cov64\t7373\t7375\t16.666667\r\n", "scaffold7_cov100\t28086\t28088\t16.666667\r\n", "scaffold7_cov100\t37936\t37938\t21.428571\r\n", "scaffold7_cov100\t40234\t40236\t40.000000\r\n", "scaffold7_cov100\t40236\t40238\t40.000000\r\n", "scaffold7_cov100\t131309\t131311\t20.000000\r\n", "scaffold7_cov100\t162610\t162612\t30.000000\r\n", "scaffold7_cov100\t169073\t169075\t37.500000\r\n", "\r\n", "==> Meth6_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-paFlanks <==\r\n", "scaffold6_cov64\t5797\t5799\t0.550747\r\n", "scaffold6_cov64\t5800\t5802\t0.864780\r\n", "scaffold6_cov64\t6690\t6692\t0.000000\r\n", "scaffold6_cov64\t6732\t6734\t0.000000\r\n", "scaffold6_cov64\t6751\t6753\t0.000000\r\n", "scaffold6_cov64\t6805\t6807\t0.000000\r\n", "scaffold6_cov64\t6813\t6815\t0.000000\r\n", "scaffold6_cov64\t6862\t6864\t0.000000\r\n", "scaffold6_cov64\t6880\t6882\t0.000000\r\n", "scaffold6_cov64\t7263\t7265\t0.000000\r\n", "\r\n", "==> Meth6_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-paFlanks <==\r\n", "scaffold6_cov64\t5797\t5799\t0.550747\r\n", "scaffold6_cov64\t5800\t5802\t0.864780\r\n", "scaffold6_cov64\t6687\t6689\t14.285714\r\n", "scaffold6_cov64\t6690\t6692\t0.000000\r\n", "scaffold6_cov64\t6704\t6706\t14.285714\r\n", "scaffold6_cov64\t6732\t6734\t0.000000\r\n", "scaffold6_cov64\t6751\t6753\t0.000000\r\n", "scaffold6_cov64\t6805\t6807\t0.000000\r\n", "scaffold6_cov64\t6813\t6815\t0.000000\r\n", "scaffold6_cov64\t6862\t6864\t0.000000\r\n", "\r\n", "==> Meth7_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-paFlanks <==\r\n", "scaffold7_cov100\t6231\t6233\t97.142857\r\n", "scaffold7_cov100\t6233\t6235\t97.222222\r\n", "scaffold7_cov100\t12652\t12654\t81.818182\r\n", "scaffold7_cov100\t12662\t12664\t80.000000\r\n", "scaffold7_cov100\t12675\t12677\t82.608696\r\n", "scaffold7_cov100\t12683\t12685\t91.304348\r\n", "scaffold7_cov100\t12704\t12706\t76.470588\r\n", "scaffold7_cov100\t12726\t12728\t78.571429\r\n", "scaffold7_cov100\t12737\t12739\t78.571429\r\n", "scaffold7_cov100\t12806\t12808\t90.909091\r\n", "\r\n", "==> Meth7_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-paFlanks <==\r\n", "scaffold6_cov64\t6805\t6807\t14.285714\r\n", "scaffold6_cov64\t6880\t6882\t14.285714\r\n", "scaffold6_cov64\t7609\t7611\t14.285714\r\n", "scaffold7_cov100\t12821\t12823\t36.363636\r\n", "scaffold7_cov100\t12861\t12863\t40.000000\r\n", "scaffold7_cov100\t15597\t15599\t14.285714\r\n", "scaffold7_cov100\t15614\t15616\t12.500000\r\n", "scaffold7_cov100\t24614\t24616\t42.857143\r\n", "scaffold7_cov100\t24617\t24619\t14.285714\r\n", "scaffold7_cov100\t24690\t24692\t20.000000\r\n", "\r\n", "==> Meth7_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-paFlanks <==\r\n", "scaffold6_cov64\t5797\t5799\t0.000000\r\n", "scaffold6_cov64\t5800\t5802\t7.692308\r\n", "scaffold6_cov64\t6813\t6815\t0.000000\r\n", "scaffold6_cov64\t6862\t6864\t0.000000\r\n", "scaffold6_cov64\t6885\t6887\t0.000000\r\n", "scaffold6_cov64\t7097\t7099\t0.000000\r\n", "scaffold6_cov64\t7159\t7161\t0.000000\r\n", "scaffold6_cov64\t7163\t7165\t0.000000\r\n", "scaffold6_cov64\t7165\t7167\t0.000000\r\n", "scaffold6_cov64\t7177\t7179\t0.000000\r\n", "\r\n", "==> Meth7_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-paFlanks <==\r\n", "scaffold6_cov64\t5797\t5799\t0.000000\r\n", "scaffold6_cov64\t5800\t5802\t7.692308\r\n", "scaffold6_cov64\t6805\t6807\t14.285714\r\n", "scaffold6_cov64\t6813\t6815\t0.000000\r\n", "scaffold6_cov64\t6862\t6864\t0.000000\r\n", "scaffold6_cov64\t6880\t6882\t14.285714\r\n", "scaffold6_cov64\t6885\t6887\t0.000000\r\n", "scaffold6_cov64\t7097\t7099\t0.000000\r\n", "scaffold6_cov64\t7159\t7161\t0.000000\r\n", "scaffold6_cov64\t7163\t7165\t0.000000\r\n", "\r\n", "==> Meth8_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-paFlanks <==\r\n", "scaffold7_cov100\t6233\t6235\t93.103448\r\n", "scaffold7_cov100\t12652\t12654\t96.226415\r\n", "scaffold7_cov100\t12662\t12664\t92.079208\r\n", "scaffold7_cov100\t12675\t12677\t92.307692\r\n", "scaffold7_cov100\t12683\t12685\t92.134831\r\n", "scaffold7_cov100\t12704\t12706\t66.666667\r\n", "scaffold7_cov100\t12726\t12728\t59.459459\r\n", "scaffold7_cov100\t12737\t12739\t83.582090\r\n", "scaffold7_cov100\t12806\t12808\t91.176471\r\n", "scaffold7_cov100\t12808\t12810\t91.176471\r\n", "\r\n", "==> Meth8_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-paFlanks <==\r\n", "scaffold7_cov100\t6231\t6233\t42.857143\r\n", "scaffold7_cov100\t12131\t12133\t40.000000\r\n", "scaffold7_cov100\t12247\t12249\t37.500000\r\n", "scaffold7_cov100\t12861\t12863\t27.272727\r\n", "scaffold7_cov100\t24494\t24496\t17.647059\r\n", "scaffold7_cov100\t24830\t24832\t16.666667\r\n", "scaffold7_cov100\t24895\t24897\t20.000000\r\n", "scaffold7_cov100\t83540\t83542\t20.000000\r\n", "scaffold7_cov100\t92019\t92021\t33.333333\r\n", "scaffold7_cov100\t92029\t92031\t44.444444\r\n", "\r\n", "==> Meth8_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-paFlanks <==\r\n", "scaffold7_cov100\t12587\t12589\t0.840336\r\n", "scaffold7_cov100\t13038\t13040\t3.448276\r\n", "scaffold7_cov100\t24617\t24619\t0.000000\r\n", "scaffold7_cov100\t24690\t24692\t0.000000\r\n", "scaffold7_cov100\t83512\t83514\t0.000000\r\n", "scaffold7_cov100\t83535\t83537\t0.000000\r\n", "scaffold7_cov100\t83538\t83540\t0.000000\r\n", "scaffold7_cov100\t83552\t83554\t0.000000\r\n", "scaffold7_cov100\t83554\t83556\t0.000000\r\n", "scaffold7_cov100\t99015\t99017\t0.000000\r\n", "\r\n", "==> Meth8_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-paFlanks <==\r\n", "scaffold7_cov100\t6231\t6233\t42.857143\r\n", "scaffold7_cov100\t6233\t6235\t93.103448\r\n", "scaffold7_cov100\t12131\t12133\t40.000000\r\n", "scaffold7_cov100\t12247\t12249\t37.500000\r\n", "scaffold7_cov100\t12587\t12589\t0.840336\r\n", "scaffold7_cov100\t12652\t12654\t96.226415\r\n", "scaffold7_cov100\t12662\t12664\t92.079208\r\n", "scaffold7_cov100\t12675\t12677\t92.307692\r\n", "scaffold7_cov100\t12683\t12685\t92.134831\r\n", "scaffold7_cov100\t12704\t12706\t66.666667\r\n", "\r\n", "==> Meth9_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-paFlanks <==\r\n", "scaffold7_cov100\t6231\t6233\t95.555556\r\n", "scaffold7_cov100\t6233\t6235\t97.619048\r\n", "scaffold7_cov100\t11815\t11817\t90.000000\r\n", "scaffold7_cov100\t12652\t12654\t90.909091\r\n", "scaffold7_cov100\t12662\t12664\t80.000000\r\n", "scaffold7_cov100\t12675\t12677\t80.000000\r\n", "scaffold7_cov100\t12704\t12706\t50.000000\r\n", "scaffold7_cov100\t12726\t12728\t57.142857\r\n", "scaffold7_cov100\t12857\t12859\t60.000000\r\n", "scaffold7_cov100\t19284\t19286\t94.318182\r\n", "\r\n", "==> Meth9_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-paFlanks <==\r\n", "scaffold7_cov100\t12587\t12589\t12.500000\r\n", "scaffold7_cov100\t12683\t12685\t40.000000\r\n", "scaffold7_cov100\t12737\t12739\t28.571429\r\n", "scaffold7_cov100\t12821\t12823\t42.857143\r\n", "scaffold7_cov100\t12861\t12863\t20.000000\r\n", "scaffold7_cov100\t13275\t13277\t47.619048\r\n", "scaffold7_cov100\t15622\t15624\t16.666667\r\n", "scaffold7_cov100\t15630\t15632\t14.285714\r\n", "scaffold7_cov100\t24614\t24616\t47.619048\r\n", "scaffold7_cov100\t24617\t24619\t42.857143\r\n", "\r\n", "==> Meth9_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-paFlanks <==\r\n", "scaffold6_cov64\t5797\t5799\t0.000000\r\n", "scaffold6_cov64\t5800\t5802\t0.000000\r\n", "scaffold6_cov64\t6751\t6753\t0.000000\r\n", "scaffold6_cov64\t6805\t6807\t0.000000\r\n", "scaffold6_cov64\t6813\t6815\t0.000000\r\n", "scaffold6_cov64\t6862\t6864\t0.000000\r\n", "scaffold6_cov64\t6880\t6882\t7.142857\r\n", "scaffold6_cov64\t6885\t6887\t0.000000\r\n", "scaffold6_cov64\t6909\t6911\t0.000000\r\n", "scaffold6_cov64\t6943\t6945\t0.000000\r\n", "\r\n", "==> Meth9_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-paFlanks <==\r\n", "scaffold6_cov64\t5797\t5799\t0.000000\r\n", "scaffold6_cov64\t5800\t5802\t0.000000\r\n", "scaffold6_cov64\t6751\t6753\t0.000000\r\n", "scaffold6_cov64\t6805\t6807\t0.000000\r\n", "scaffold6_cov64\t6813\t6815\t0.000000\r\n", "scaffold6_cov64\t6862\t6864\t0.000000\r\n", "scaffold6_cov64\t6880\t6882\t7.142857\r\n", "scaffold6_cov64\t6885\t6887\t0.000000\r\n", "scaffold6_cov64\t6909\t6911\t0.000000\r\n", "scaffold6_cov64\t6943\t6945\t0.000000\r\n" ] } ], "source": [ "#Check output\n", "!head *paFlanks" ] }, { "cell_type": "code", "execution_count": 205, "metadata": { "collapsed": false, "scrolled": true }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ " 19148 Meth1_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-paFlanks\n", " 73346 Meth1_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-paFlanks\n", " 1018940 Meth1_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-paFlanks\n", " 1111434 Meth1_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-paFlanks\n", " 22078 Meth2_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-paFlanks\n", " 69879 Meth2_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-paFlanks\n", " 1189855 Meth2_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-paFlanks\n", " 1281812 Meth2_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-paFlanks\n", " 21825 Meth3_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-paFlanks\n", " 76679 Meth3_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-paFlanks\n", " 1078982 Meth3_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-paFlanks\n", " 1177486 Meth3_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-paFlanks\n", " 5512 Meth4_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-paFlanks\n", " 25985 Meth4_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-paFlanks\n", " 332396 Meth4_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-paFlanks\n", " 363893 Meth4_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-paFlanks\n", " 5537 Meth5_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-paFlanks\n", " 12401 Meth5_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-paFlanks\n", " 271274 Meth5_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-paFlanks\n", " 289212 Meth5_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-paFlanks\n", " 4609 Meth6_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-paFlanks\n", " 16818 Meth6_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-paFlanks\n", " 279752 Meth6_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-paFlanks\n", " 301179 Meth6_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-paFlanks\n", " 41653 Meth7_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-paFlanks\n", " 50998 Meth7_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-paFlanks\n", " 375763 Meth7_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-paFlanks\n", " 468414 Meth7_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-paFlanks\n", " 32905 Meth8_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-paFlanks\n", " 12312 Meth8_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-paFlanks\n", " 34885 Meth8_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-paFlanks\n", " 80102 Meth8_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-paFlanks\n", " 42444 Meth9_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-paFlanks\n", " 58605 Meth9_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-paFlanks\n", " 395780 Meth9_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-paFlanks\n", " 496829 Meth9_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-paFlanks\n", " 11140722 total\n" ] } ], "source": [ "#Count number of overlaps\n", "!wc -l *paFlanks" ] }, { "cell_type": "code", "execution_count": 206, "metadata": { "collapsed": true }, "outputs": [], "source": [ "!wc -l *paFlanks > Pact-5x-paFlanks-counts.txt" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "#### 4f. Upstream flanking regions" ] }, { "cell_type": "code", "execution_count": 207, "metadata": { "collapsed": true, "scrolled": true }, "outputs": [], "source": [ "%%bash\n", "\n", "for f in *bed\n", "do\n", " /usr/local/bin/intersectBed \\\n", " -u \\\n", " -a ${f} \\\n", " -b ../../../genome-feature-files/Pact.GFFannotation.flanks.Upstream.gff \\\n", " > ${f}-paFlanksUpstream\n", "done" ] }, { "cell_type": "code", "execution_count": 208, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "==> Meth1_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-paFlanksUpstream <==\r\n", "scaffold7_cov100\t6231\t6233\t100.000000\r\n", "scaffold7_cov100\t6233\t6235\t100.000000\r\n", "scaffold7_cov100\t19284\t19286\t85.714286\r\n", "scaffold7_cov100\t19296\t19298\t100.000000\r\n", "scaffold7_cov100\t77986\t77988\t80.000000\r\n", "scaffold7_cov100\t78473\t78475\t72.727273\r\n", "scaffold7_cov100\t101651\t101653\t60.000000\r\n", "scaffold7_cov100\t101750\t101752\t50.000000\r\n", "scaffold7_cov100\t108138\t108140\t72.727273\r\n", "scaffold7_cov100\t108821\t108823\t50.000000\r\n", "\r\n", "==> Meth1_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-paFlanksUpstream <==\r\n", "scaffold7_cov100\t15597\t15599\t33.333333\r\n", "scaffold7_cov100\t30593\t30595\t11.111111\r\n", "scaffold7_cov100\t30680\t30682\t11.111111\r\n", "scaffold7_cov100\t30695\t30697\t25.000000\r\n", "scaffold7_cov100\t37862\t37864\t14.285714\r\n", "scaffold7_cov100\t38168\t38170\t14.285714\r\n", "scaffold7_cov100\t38701\t38703\t20.000000\r\n", "scaffold7_cov100\t41045\t41047\t11.111111\r\n", "scaffold7_cov100\t49670\t49672\t11.111111\r\n", "scaffold7_cov100\t79910\t79912\t37.500000\r\n", "\r\n", "==> Meth1_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-paFlanksUpstream <==\r\n", "scaffold6_cov64\t5797\t5799\t3.125000\r\n", "scaffold6_cov64\t5800\t5802\t3.030303\r\n", "scaffold7_cov100\t6764\t6766\t0.000000\r\n", "scaffold7_cov100\t6913\t6915\t0.000000\r\n", "scaffold7_cov100\t12247\t12249\t0.000000\r\n", "scaffold7_cov100\t15549\t15551\t0.000000\r\n", "scaffold7_cov100\t15569\t15571\t0.000000\r\n", "scaffold7_cov100\t15609\t15611\t0.000000\r\n", "scaffold7_cov100\t15614\t15616\t0.000000\r\n", "scaffold7_cov100\t15622\t15624\t0.000000\r\n", "\r\n", "==> Meth1_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-paFlanksUpstream <==\r\n", "scaffold6_cov64\t5797\t5799\t3.125000\r\n", "scaffold6_cov64\t5800\t5802\t3.030303\r\n", "scaffold7_cov100\t6231\t6233\t100.000000\r\n", "scaffold7_cov100\t6233\t6235\t100.000000\r\n", "scaffold7_cov100\t6764\t6766\t0.000000\r\n", "scaffold7_cov100\t6913\t6915\t0.000000\r\n", "scaffold7_cov100\t12247\t12249\t0.000000\r\n", "scaffold7_cov100\t15549\t15551\t0.000000\r\n", "scaffold7_cov100\t15569\t15571\t0.000000\r\n", "scaffold7_cov100\t15597\t15599\t33.333333\r\n", "\r\n", "==> Meth2_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-paFlanksUpstream <==\r\n", "scaffold7_cov100\t6231\t6233\t71.428571\r\n", "scaffold7_cov100\t6233\t6235\t100.000000\r\n", "scaffold7_cov100\t11815\t11817\t77.777778\r\n", "scaffold7_cov100\t12247\t12249\t54.545455\r\n", "scaffold7_cov100\t19284\t19286\t92.307692\r\n", "scaffold7_cov100\t19296\t19298\t92.857143\r\n", "scaffold7_cov100\t77986\t77988\t81.818182\r\n", "scaffold7_cov100\t77988\t77990\t100.000000\r\n", "scaffold7_cov100\t78473\t78475\t58.333333\r\n", "scaffold7_cov100\t101750\t101752\t66.666667\r\n", "\r\n", "==> Meth2_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-paFlanksUpstream <==\r\n", "scaffold7_cov100\t12131\t12133\t28.571429\r\n", "scaffold7_cov100\t18520\t18522\t20.000000\r\n", "scaffold7_cov100\t38701\t38703\t14.285714\r\n", "scaffold7_cov100\t41004\t41006\t14.285714\r\n", "scaffold7_cov100\t67717\t67719\t14.285714\r\n", "scaffold7_cov100\t68081\t68083\t20.000000\r\n", "scaffold7_cov100\t73672\t73674\t16.666667\r\n", "scaffold7_cov100\t78386\t78388\t25.000000\r\n", "scaffold7_cov100\t80016\t80018\t15.384615\r\n", "scaffold7_cov100\t83659\t83661\t15.384615\r\n", "\r\n", "==> Meth2_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-paFlanksUpstream <==\r\n", "scaffold6_cov64\t5797\t5799\t0.000000\r\n", "scaffold6_cov64\t5800\t5802\t0.000000\r\n", "scaffold7_cov100\t6764\t6766\t0.000000\r\n", "scaffold7_cov100\t6913\t6915\t7.142857\r\n", "scaffold7_cov100\t12587\t12589\t0.000000\r\n", "scaffold7_cov100\t15549\t15551\t0.000000\r\n", "scaffold7_cov100\t15569\t15571\t0.000000\r\n", "scaffold7_cov100\t15597\t15599\t0.000000\r\n", "scaffold7_cov100\t15609\t15611\t0.000000\r\n", "scaffold7_cov100\t15614\t15616\t0.000000\r\n", "\r\n", "==> Meth2_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-paFlanksUpstream <==\r\n", "scaffold6_cov64\t5797\t5799\t0.000000\r\n", "scaffold6_cov64\t5800\t5802\t0.000000\r\n", "scaffold7_cov100\t6231\t6233\t71.428571\r\n", "scaffold7_cov100\t6233\t6235\t100.000000\r\n", "scaffold7_cov100\t6764\t6766\t0.000000\r\n", "scaffold7_cov100\t6913\t6915\t7.142857\r\n", "scaffold7_cov100\t11815\t11817\t77.777778\r\n", "scaffold7_cov100\t12131\t12133\t28.571429\r\n", "scaffold7_cov100\t12247\t12249\t54.545455\r\n", "scaffold7_cov100\t12587\t12589\t0.000000\r\n", "\r\n", "==> Meth3_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-paFlanksUpstream <==\r\n", "scaffold7_cov100\t6231\t6233\t100.000000\r\n", "scaffold7_cov100\t6233\t6235\t100.000000\r\n", "scaffold7_cov100\t11815\t11817\t50.000000\r\n", "scaffold7_cov100\t18520\t18522\t66.666667\r\n", "scaffold7_cov100\t19284\t19286\t80.000000\r\n", "scaffold7_cov100\t19296\t19298\t88.888889\r\n", "scaffold7_cov100\t77986\t77988\t70.000000\r\n", "scaffold7_cov100\t77988\t77990\t100.000000\r\n", "scaffold7_cov100\t78473\t78475\t55.555556\r\n", "scaffold7_cov100\t99015\t99017\t54.545455\r\n", "\r\n", "==> Meth3_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-paFlanksUpstream <==\r\n", "scaffold7_cov100\t29923\t29925\t12.500000\r\n", "scaffold7_cov100\t29931\t29933\t11.111111\r\n", "scaffold7_cov100\t30141\t30143\t12.500000\r\n", "scaffold7_cov100\t30252\t30254\t20.000000\r\n", "scaffold7_cov100\t49411\t49413\t14.285714\r\n", "scaffold7_cov100\t49637\t49639\t16.666667\r\n", "scaffold7_cov100\t67546\t67548\t12.500000\r\n", "scaffold7_cov100\t79910\t79912\t42.857143\r\n", "scaffold7_cov100\t82907\t82909\t14.285714\r\n", "scaffold7_cov100\t82971\t82973\t16.666667\r\n", "\r\n", "==> Meth3_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-paFlanksUpstream <==\r\n", "scaffold6_cov64\t5797\t5799\t0.000000\r\n", "scaffold6_cov64\t5800\t5802\t0.000000\r\n", "scaffold7_cov100\t6764\t6766\t0.000000\r\n", "scaffold7_cov100\t6913\t6915\t0.000000\r\n", "scaffold7_cov100\t12131\t12133\t0.000000\r\n", "scaffold7_cov100\t15549\t15551\t0.000000\r\n", "scaffold7_cov100\t15569\t15571\t0.000000\r\n", "scaffold7_cov100\t15597\t15599\t0.000000\r\n", "scaffold7_cov100\t15609\t15611\t0.000000\r\n", "scaffold7_cov100\t15614\t15616\t0.000000\r\n", "\r\n", "==> Meth3_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-paFlanksUpstream <==\r\n", "scaffold6_cov64\t5797\t5799\t0.000000\r\n", "scaffold6_cov64\t5800\t5802\t0.000000\r\n", "scaffold7_cov100\t6231\t6233\t100.000000\r\n", "scaffold7_cov100\t6233\t6235\t100.000000\r\n", "scaffold7_cov100\t6764\t6766\t0.000000\r\n", "scaffold7_cov100\t6913\t6915\t0.000000\r\n", "scaffold7_cov100\t11815\t11817\t50.000000\r\n", "scaffold7_cov100\t12131\t12133\t0.000000\r\n", "scaffold7_cov100\t15549\t15551\t0.000000\r\n", "scaffold7_cov100\t15569\t15571\t0.000000\r\n", "\r\n", "==> Meth4_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-paFlanksUpstream <==\r\n", "scaffold7_cov100\t40896\t40898\t50.000000\r\n", "scaffold7_cov100\t342219\t342221\t50.000000\r\n", "scaffold20_cov103\t50562\t50564\t60.000000\r\n", "scaffold20_cov103\t69200\t69202\t100.000000\r\n", "scaffold20_cov103\t86601\t86603\t100.000000\r\n", "scaffold28_cov97\t38683\t38685\t50.000000\r\n", "scaffold28_cov97\t72248\t72250\t60.000000\r\n", "scaffold41_cov106\t22329\t22331\t76.000000\r\n", "scaffold42_cov106\t33801\t33803\t66.666667\r\n", "scaffold42_cov106\t192040\t192042\t100.000000\r\n", "\r\n", "==> Meth4_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-paFlanksUpstream <==\r\n", "scaffold7_cov100\t38369\t38371\t11.111111\r\n", "scaffold7_cov100\t40816\t40818\t40.000000\r\n", "scaffold7_cov100\t40898\t40900\t16.666667\r\n", "scaffold7_cov100\t40917\t40919\t20.000000\r\n", "scaffold7_cov100\t40936\t40938\t20.000000\r\n", "scaffold7_cov100\t49302\t49304\t42.857143\r\n", "scaffold7_cov100\t49331\t49333\t37.500000\r\n", "scaffold7_cov100\t49341\t49343\t37.500000\r\n", "scaffold7_cov100\t49347\t49349\t33.333333\r\n", "scaffold7_cov100\t49349\t49351\t33.333333\r\n", "\r\n", "==> Meth4_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-paFlanksUpstream <==\r\n", "scaffold6_cov64\t5797\t5799\t0.629811\r\n", "scaffold6_cov64\t5800\t5802\t0.700771\r\n", "scaffold7_cov100\t6764\t6766\t0.000000\r\n", "scaffold7_cov100\t15732\t15734\t0.000000\r\n", "scaffold7_cov100\t15735\t15737\t0.000000\r\n", "scaffold7_cov100\t30584\t30586\t0.000000\r\n", "scaffold7_cov100\t30593\t30595\t0.000000\r\n", "scaffold7_cov100\t30597\t30599\t0.000000\r\n", "scaffold7_cov100\t30680\t30682\t0.000000\r\n", "scaffold7_cov100\t30695\t30697\t0.000000\r\n", "\r\n", "==> Meth4_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-paFlanksUpstream <==\r\n", "scaffold6_cov64\t5797\t5799\t0.629811\r\n", "scaffold6_cov64\t5800\t5802\t0.700771\r\n", "scaffold7_cov100\t6764\t6766\t0.000000\r\n", "scaffold7_cov100\t15732\t15734\t0.000000\r\n", "scaffold7_cov100\t15735\t15737\t0.000000\r\n", "scaffold7_cov100\t30584\t30586\t0.000000\r\n", "scaffold7_cov100\t30593\t30595\t0.000000\r\n", "scaffold7_cov100\t30597\t30599\t0.000000\r\n", "scaffold7_cov100\t30680\t30682\t0.000000\r\n", "scaffold7_cov100\t30695\t30697\t0.000000\r\n", "\r\n", "==> Meth5_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-paFlanksUpstream <==\r\n", "scaffold7_cov100\t92029\t92031\t100.000000\r\n", "scaffold7_cov100\t151631\t151633\t50.000000\r\n", "scaffold7_cov100\t219436\t219438\t57.142857\r\n", "scaffold7_cov100\t281483\t281485\t60.000000\r\n", "scaffold7_cov100\t281501\t281503\t60.000000\r\n", "scaffold7_cov100\t342219\t342221\t88.888889\r\n", "scaffold7_cov100\t386168\t386170\t50.000000\r\n", "scaffold7_cov100\t477140\t477142\t60.000000\r\n", "scaffold19_cov103\t94546\t94548\t75.000000\r\n", "scaffold19_cov103\t148422\t148424\t50.000000\r\n", "\r\n", "==> Meth5_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-paFlanksUpstream <==\r\n", "scaffold7_cov100\t91999\t92001\t14.285714\r\n", "scaffold7_cov100\t116515\t116517\t20.000000\r\n", "scaffold7_cov100\t162610\t162612\t20.000000\r\n", "scaffold7_cov100\t198799\t198801\t14.285714\r\n", "scaffold7_cov100\t210084\t210086\t22.222222\r\n", "scaffold7_cov100\t219440\t219442\t20.000000\r\n", "scaffold7_cov100\t259165\t259167\t16.666667\r\n", "scaffold7_cov100\t259473\t259475\t22.222222\r\n", "scaffold7_cov100\t271716\t271718\t25.000000\r\n", "scaffold7_cov100\t331397\t331399\t37.500000\r\n", "\r\n", "==> Meth5_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-paFlanksUpstream <==\r\n", "scaffold6_cov64\t5797\t5799\t0.654664\r\n", "scaffold6_cov64\t5800\t5802\t0.572988\r\n", "scaffold7_cov100\t15668\t15670\t0.000000\r\n", "scaffold7_cov100\t15670\t15672\t0.000000\r\n", "scaffold7_cov100\t15715\t15717\t0.000000\r\n", "scaffold7_cov100\t15724\t15726\t0.000000\r\n", "scaffold7_cov100\t15732\t15734\t0.000000\r\n", "scaffold7_cov100\t30584\t30586\t0.000000\r\n", "scaffold7_cov100\t30593\t30595\t0.000000\r\n", "scaffold7_cov100\t30597\t30599\t0.000000\r\n", "\r\n", "==> Meth5_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-paFlanksUpstream <==\r\n", "scaffold6_cov64\t5797\t5799\t0.654664\r", "\r\n", "scaffold6_cov64\t5800\t5802\t0.572988\r\n", "scaffold7_cov100\t15668\t15670\t0.000000\r\n", "scaffold7_cov100\t15670\t15672\t0.000000\r\n", "scaffold7_cov100\t15715\t15717\t0.000000\r\n", "scaffold7_cov100\t15724\t15726\t0.000000\r\n", "scaffold7_cov100\t15732\t15734\t0.000000\r\n", "scaffold7_cov100\t30584\t30586\t0.000000\r\n", "scaffold7_cov100\t30593\t30595\t0.000000\r\n", "scaffold7_cov100\t30597\t30599\t0.000000\r\n", "\r\n", "==> Meth6_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-paFlanksUpstream <==\r\n", "scaffold7_cov100\t151631\t151633\t60.000000\r\n", "scaffold7_cov100\t210167\t210169\t83.333333\r\n", "scaffold7_cov100\t281483\t281485\t50.000000\r\n", "scaffold7_cov100\t281501\t281503\t55.555556\r\n", "scaffold19_cov103\t94546\t94548\t50.000000\r\n", "scaffold19_cov103\t148521\t148523\t62.500000\r\n", "scaffold19_cov103\t148544\t148546\t62.500000\r\n", "scaffold19_cov103\t148559\t148561\t62.500000\r\n", "scaffold20_cov103\t69200\t69202\t98.039216\r\n", "scaffold21_cov102\t5653\t5655\t87.500000\r\n", "\r\n", "==> Meth6_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-paFlanksUpstream <==\r\n", "scaffold7_cov100\t37936\t37938\t21.428571\r\n", "scaffold7_cov100\t40234\t40236\t40.000000\r\n", "scaffold7_cov100\t40236\t40238\t40.000000\r\n", "scaffold7_cov100\t162610\t162612\t30.000000\r\n", "scaffold7_cov100\t188197\t188199\t11.111111\r\n", "scaffold7_cov100\t214344\t214346\t28.571429\r\n", "scaffold7_cov100\t219436\t219438\t18.181818\r\n", "scaffold7_cov100\t219440\t219442\t18.181818\r\n", "scaffold7_cov100\t219497\t219499\t40.000000\r\n", "scaffold7_cov100\t282891\t282893\t11.904762\r\n", "\r\n", "==> Meth6_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-paFlanksUpstream <==\r\n", "scaffold6_cov64\t5797\t5799\t0.550747\r\n", "scaffold6_cov64\t5800\t5802\t0.864780\r\n", "scaffold7_cov100\t15732\t15734\t0.000000\r\n", "scaffold7_cov100\t15735\t15737\t0.000000\r\n", "scaffold7_cov100\t30584\t30586\t0.000000\r\n", "scaffold7_cov100\t30593\t30595\t0.000000\r\n", "scaffold7_cov100\t30597\t30599\t0.000000\r\n", "scaffold7_cov100\t30680\t30682\t0.000000\r\n", "scaffold7_cov100\t30695\t30697\t0.000000\r\n", "scaffold7_cov100\t30731\t30733\t0.000000\r\n", "\r\n", "==> Meth6_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-paFlanksUpstream <==\r\n", "scaffold6_cov64\t5797\t5799\t0.550747\r\n", "scaffold6_cov64\t5800\t5802\t0.864780\r\n", "scaffold7_cov100\t15732\t15734\t0.000000\r\n", "scaffold7_cov100\t15735\t15737\t0.000000\r\n", "scaffold7_cov100\t30584\t30586\t0.000000\r\n", "scaffold7_cov100\t30593\t30595\t0.000000\r\n", "scaffold7_cov100\t30597\t30599\t0.000000\r\n", "scaffold7_cov100\t30680\t30682\t0.000000\r\n", "scaffold7_cov100\t30695\t30697\t0.000000\r\n", "scaffold7_cov100\t30731\t30733\t0.000000\r\n", "\r\n", "==> Meth7_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-paFlanksUpstream <==\r\n", "scaffold7_cov100\t6231\t6233\t97.142857\r\n", "scaffold7_cov100\t6233\t6235\t97.222222\r\n", "scaffold7_cov100\t12652\t12654\t81.818182\r\n", "scaffold7_cov100\t12662\t12664\t80.000000\r\n", "scaffold7_cov100\t18520\t18522\t60.000000\r\n", "scaffold7_cov100\t19284\t19286\t93.577982\r\n", "scaffold7_cov100\t19296\t19298\t94.174757\r\n", "scaffold7_cov100\t77986\t77988\t77.777778\r\n", "scaffold7_cov100\t77988\t77990\t82.352941\r\n", "scaffold7_cov100\t92060\t92062\t50.000000\r\n", "\r\n", "==> Meth7_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-paFlanksUpstream <==\r\n", "scaffold7_cov100\t15597\t15599\t14.285714\r\n", "scaffold7_cov100\t15614\t15616\t12.500000\r\n", "scaffold7_cov100\t41134\t41136\t20.000000\r\n", "scaffold7_cov100\t49521\t49523\t11.111111\r\n", "scaffold7_cov100\t67437\t67439\t11.111111\r\n", "scaffold7_cov100\t67610\t67612\t14.285714\r\n", "scaffold7_cov100\t67616\t67618\t16.666667\r\n", "scaffold7_cov100\t73493\t73495\t16.666667\r\n", "scaffold7_cov100\t91999\t92001\t11.111111\r\n", "scaffold7_cov100\t92019\t92021\t27.272727\r\n", "\r\n", "==> Meth7_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-paFlanksUpstream <==\r\n", "scaffold6_cov64\t5797\t5799\t0.000000\r\n", "scaffold6_cov64\t5800\t5802\t7.692308\r\n", "scaffold7_cov100\t6764\t6766\t0.000000\r\n", "scaffold7_cov100\t12131\t12133\t0.000000\r\n", "scaffold7_cov100\t12247\t12249\t0.000000\r\n", "scaffold7_cov100\t12587\t12589\t0.000000\r\n", "scaffold7_cov100\t15549\t15551\t0.000000\r\n", "scaffold7_cov100\t15569\t15571\t0.000000\r\n", "scaffold7_cov100\t15609\t15611\t0.000000\r\n", "scaffold7_cov100\t15622\t15624\t0.000000\r\n", "\r\n", "==> Meth7_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-paFlanksUpstream <==\r\n", "scaffold6_cov64\t5797\t5799\t0.000000\r\n", "scaffold6_cov64\t5800\t5802\t7.692308\r\n", "scaffold7_cov100\t6231\t6233\t97.142857\r\n", "scaffold7_cov100\t6233\t6235\t97.222222\r\n", "scaffold7_cov100\t6764\t6766\t0.000000\r\n", "scaffold7_cov100\t12131\t12133\t0.000000\r\n", "scaffold7_cov100\t12247\t12249\t0.000000\r\n", "scaffold7_cov100\t12587\t12589\t0.000000\r\n", "scaffold7_cov100\t12652\t12654\t81.818182\r\n", "scaffold7_cov100\t12662\t12664\t80.000000\r\n", "\r\n", "==> Meth8_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-paFlanksUpstream <==\r\n", "scaffold7_cov100\t6233\t6235\t93.103448\r\n", "scaffold7_cov100\t12652\t12654\t96.226415\r\n", "scaffold7_cov100\t12662\t12664\t92.079208\r\n", "scaffold7_cov100\t19284\t19286\t91.891892\r\n", "scaffold7_cov100\t19296\t19298\t93.333333\r\n", "scaffold7_cov100\t92051\t92053\t66.666667\r\n", "scaffold7_cov100\t92060\t92062\t53.333333\r\n", "scaffold7_cov100\t92100\t92102\t64.285714\r\n", "scaffold7_cov100\t99087\t99089\t75.000000\r\n", "scaffold7_cov100\t332755\t332757\t100.000000\r\n", "\r\n", "==> Meth8_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-paFlanksUpstream <==\r\n", "scaffold7_cov100\t6231\t6233\t42.857143\r\n", "scaffold7_cov100\t12131\t12133\t40.000000\r\n", "scaffold7_cov100\t12247\t12249\t37.500000\r\n", "scaffold7_cov100\t83540\t83542\t20.000000\r\n", "scaffold7_cov100\t92019\t92021\t33.333333\r\n", "scaffold7_cov100\t92029\t92031\t44.444444\r\n", "scaffold7_cov100\t92055\t92057\t26.666667\r\n", "scaffold7_cov100\t92105\t92107\t41.666667\r\n", "scaffold7_cov100\t99065\t99067\t33.333333\r", "\r\n", "scaffold7_cov100\t148473\t148475\t40.000000\r\n", "\r\n", "==> Meth8_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-paFlanksUpstream <==\r\n", "scaffold7_cov100\t12587\t12589\t0.840336\r\n", "scaffold7_cov100\t83512\t83514\t0.000000\r\n", "scaffold7_cov100\t83535\t83537\t0.000000\r\n", "scaffold7_cov100\t83538\t83540\t0.000000\r\n", "scaffold7_cov100\t83552\t83554\t0.000000\r\n", "scaffold7_cov100\t83554\t83556\t0.000000\r\n", "scaffold7_cov100\t99015\t99017\t0.000000\r\n", "scaffold7_cov100\t99029\t99031\t0.000000\r\n", "scaffold7_cov100\t142752\t142754\t0.000000\r\n", "scaffold7_cov100\t254147\t254149\t0.000000\r\n", "\r\n", "==> Meth8_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-paFlanksUpstream <==\r\n", "scaffold7_cov100\t6231\t6233\t42.857143\r\n", "scaffold7_cov100\t6233\t6235\t93.103448\r\n", "scaffold7_cov100\t12131\t12133\t40.000000\r\n", "scaffold7_cov100\t12247\t12249\t37.500000\r\n", "scaffold7_cov100\t12587\t12589\t0.840336\r\n", "scaffold7_cov100\t12652\t12654\t96.226415\r\n", "scaffold7_cov100\t12662\t12664\t92.079208\r\n", "scaffold7_cov100\t19284\t19286\t91.891892\r\n", "scaffold7_cov100\t19296\t19298\t93.333333\r\n", "scaffold7_cov100\t83512\t83514\t0.000000\r\n", "\r\n", "==> Meth9_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-paFlanksUpstream <==\r\n", "scaffold7_cov100\t6231\t6233\t95.555556\r\n", "scaffold7_cov100\t6233\t6235\t97.619048\r\n", "scaffold7_cov100\t11815\t11817\t90.000000\r\n", "scaffold7_cov100\t12652\t12654\t90.909091\r\n", "scaffold7_cov100\t12662\t12664\t80.000000\r\n", "scaffold7_cov100\t19284\t19286\t94.318182\r\n", "scaffold7_cov100\t19296\t19298\t97.530864\r\n", "scaffold7_cov100\t77986\t77988\t91.666667\r\n", "scaffold7_cov100\t77988\t77990\t100.000000\r\n", "scaffold7_cov100\t92060\t92062\t50.000000\r\n", "\r\n", "==> Meth9_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-paFlanksUpstream <==\r\n", "scaffold7_cov100\t12587\t12589\t12.500000\r\n", "scaffold7_cov100\t15622\t15624\t16.666667\r\n", "scaffold7_cov100\t15630\t15632\t14.285714\r\n", "scaffold7_cov100\t38477\t38479\t20.000000\r\n", "scaffold7_cov100\t41092\t41094\t12.500000\r\n", "scaffold7_cov100\t78244\t78246\t20.000000\r\n", "scaffold7_cov100\t82965\t82967\t20.000000\r\n", "scaffold7_cov100\t82971\t82973\t20.000000\r\n", "scaffold7_cov100\t83013\t83015\t12.500000\r\n", "scaffold7_cov100\t92019\t92021\t33.333333\r\n", "\r\n", "==> Meth9_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-paFlanksUpstream <==\r\n", "scaffold6_cov64\t5797\t5799\t0.000000\r\n", "scaffold6_cov64\t5800\t5802\t0.000000\r\n", "scaffold7_cov100\t6764\t6766\t0.000000\r\n", "scaffold7_cov100\t6913\t6915\t0.000000\r\n", "scaffold7_cov100\t15638\t15640\t0.000000\r\n", "scaffold7_cov100\t29782\t29784\t0.000000\r\n", "scaffold7_cov100\t29833\t29835\t0.000000\r\n", "scaffold7_cov100\t29931\t29933\t0.000000\r\n", "scaffold7_cov100\t29983\t29985\t0.000000\r\n", "scaffold7_cov100\t29986\t29988\t0.000000\r\n", "\r\n", "==> Meth9_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-paFlanksUpstream <==\r\n", "scaffold6_cov64\t5797\t5799\t0.000000\r\n", "scaffold6_cov64\t5800\t5802\t0.000000\r\n", "scaffold7_cov100\t6231\t6233\t95.555556\r\n", "scaffold7_cov100\t6233\t6235\t97.619048\r\n", "scaffold7_cov100\t6764\t6766\t0.000000\r\n", "scaffold7_cov100\t6913\t6915\t0.000000\r\n", "scaffold7_cov100\t11815\t11817\t90.000000\r\n", "scaffold7_cov100\t12587\t12589\t12.500000\r\n", "scaffold7_cov100\t12652\t12654\t90.909091\r\n", "scaffold7_cov100\t12662\t12664\t80.000000\r\n" ] } ], "source": [ "#Check output\n", "!head *paFlanksUpstream" ] }, { "cell_type": "code", "execution_count": 209, "metadata": { "collapsed": false, "scrolled": true }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ " 11410 Meth1_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-paFlanksUpstream\n", " 44616 Meth1_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-paFlanksUpstream\n", " 630420 Meth1_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-paFlanksUpstream\n", " 686446 Meth1_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-paFlanksUpstream\n", " 12966 Meth2_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-paFlanksUpstream\n", " 41745 Meth2_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-paFlanksUpstream\n", " 733370 Meth2_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-paFlanksUpstream\n", " 788081 Meth2_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-paFlanksUpstream\n", " 12973 Meth3_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-paFlanksUpstream\n", " 46285 Meth3_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-paFlanksUpstream\n", " 667296 Meth3_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-paFlanksUpstream\n", " 726554 Meth3_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-paFlanksUpstream\n", " 3304 Meth4_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-paFlanksUpstream\n", " 16119 Meth4_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-paFlanksUpstream\n", " 213411 Meth4_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-paFlanksUpstream\n", " 232834 Meth4_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-paFlanksUpstream\n", " 3496 Meth5_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-paFlanksUpstream\n", " 7859 Meth5_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-paFlanksUpstream\n", " 175577 Meth5_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-paFlanksUpstream\n", " 186932 Meth5_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-paFlanksUpstream\n", " 2876 Meth6_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-paFlanksUpstream\n", " 10651 Meth6_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-paFlanksUpstream\n", " 180292 Meth6_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-paFlanksUpstream\n", " 193819 Meth6_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-paFlanksUpstream\n", " 25318 Meth7_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-paFlanksUpstream\n", " 32050 Meth7_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-paFlanksUpstream\n", " 240520 Meth7_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-paFlanksUpstream\n", " 297888 Meth7_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-paFlanksUpstream\n", " 20249 Meth8_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-paFlanksUpstream\n", " 7922 Meth8_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-paFlanksUpstream\n", " 22550 Meth8_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-paFlanksUpstream\n", " 50721 Meth8_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-paFlanksUpstream\n", " 25567 Meth9_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-paFlanksUpstream\n", " 36479 Meth9_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-paFlanksUpstream\n", " 252766 Meth9_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-paFlanksUpstream\n", " 314812 Meth9_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-paFlanksUpstream\n", " 6956174 total\n" ] } ], "source": [ "#Count number of overlaps\n", "!wc -l *paFlanksUpstream" ] }, { "cell_type": "code", "execution_count": 210, "metadata": { "collapsed": true }, "outputs": [], "source": [ "!wc -l *paFlanksUpstream > Pact-5x-paFlanksUpstream-counts.txt" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "#### 4g. Downstream flanking regions" ] }, { "cell_type": "code", "execution_count": 211, "metadata": { "collapsed": true, "scrolled": true }, "outputs": [], "source": [ "%%bash\n", "\n", "for f in *bed\n", "do\n", " /usr/local/bin/intersectBed \\\n", " -u \\\n", " -a ${f} \\\n", " -b ../../../genome-feature-files/Pact.GFFannotation.flanks.Downstream.gff \\\n", " > ${f}-paFlanksDownstream\n", "done" ] }, { "cell_type": "code", "execution_count": 212, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "==> Meth1_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-paFlanksDownstream <==\n", "scaffold7_cov100\t6231\t6233\t100.000000\n", "scaffold7_cov100\t6233\t6235\t100.000000\n", "scaffold7_cov100\t19284\t19286\t85.714286\n", "scaffold7_cov100\t19296\t19298\t100.000000\n", "scaffold7_cov100\t24494\t24496\t60.000000\n", "scaffold7_cov100\t24509\t24511\t88.888889\n", "scaffold7_cov100\t24557\t24559\t50.000000\n", "scaffold7_cov100\t24617\t24619\t66.666667\n", "scaffold7_cov100\t24895\t24897\t85.714286\n", "scaffold7_cov100\t24941\t24943\t72.727273\n", "\n", "==> Meth1_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-paFlanksDownstream <==\n", "scaffold6_cov64\t7373\t7375\t12.500000\n", "scaffold7_cov100\t13275\t13277\t40.000000\n", "scaffold7_cov100\t24454\t24456\t36.363636\n", "scaffold7_cov100\t24614\t24616\t22.222222\n", "scaffold7_cov100\t24769\t24771\t40.000000\n", "scaffold7_cov100\t24830\t24832\t28.571429\n", "scaffold7_cov100\t25157\t25159\t16.666667\n", "scaffold7_cov100\t28495\t28497\t12.500000\n", "scaffold7_cov100\t31789\t31791\t18.181818\n", "scaffold7_cov100\t63791\t63793\t16.666667\n", "\n", "==> Meth1_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-paFlanksDownstream <==\n", "scaffold6_cov64\t6704\t6706\t0.000000\n", "scaffold6_cov64\t6751\t6753\t0.000000\n", "scaffold6_cov64\t6805\t6807\t0.000000\n", "scaffold6_cov64\t6813\t6815\t0.000000\n", "scaffold6_cov64\t6862\t6864\t0.000000\n", "scaffold6_cov64\t6880\t6882\t0.000000\n", "scaffold6_cov64\t6885\t6887\t0.000000\n", "scaffold6_cov64\t6909\t6911\t0.000000\n", "scaffold6_cov64\t6943\t6945\t0.000000\n", "scaffold6_cov64\t6991\t6993\t0.000000\n", "\n", "==> Meth1_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-paFlanksDownstream <==\n", "scaffold6_cov64\t6704\t6706\t0.000000\n", "scaffold6_cov64\t6751\t6753\t0.000000\n", "scaffold6_cov64\t6805\t6807\t0.000000\n", "scaffold6_cov64\t6813\t6815\t0.000000\n", "scaffold6_cov64\t6862\t6864\t0.000000\n", "scaffold6_cov64\t6880\t6882\t0.000000\n", "scaffold6_cov64\t6885\t6887\t0.000000\n", "scaffold6_cov64\t6909\t6911\t0.000000\n", "scaffold6_cov64\t6943\t6945\t0.000000\n", "scaffold6_cov64\t6991\t6993\t0.000000\n", "\n", "==> Meth2_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-paFlanksDownstream <==\n", "scaffold7_cov100\t6231\t6233\t71.428571\n", "scaffold7_cov100\t6233\t6235\t100.000000\n", "scaffold7_cov100\t13275\t13277\t100.000000\n", "scaffold7_cov100\t19284\t19286\t92.307692\n", "scaffold7_cov100\t19296\t19298\t92.857143\n", "scaffold7_cov100\t24401\t24403\t100.000000\n", "scaffold7_cov100\t24443\t24445\t66.666667\n", "scaffold7_cov100\t24454\t24456\t100.000000\n", "scaffold7_cov100\t24509\t24511\t75.000000\n", "scaffold7_cov100\t24614\t24616\t93.750000\n", "\n", "==> Meth2_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-paFlanksDownstream <==\n", "scaffold6_cov64\t7077\t7079\t12.500000\n", "scaffold7_cov100\t2652\t2654\t16.666667\n", "scaffold7_cov100\t18520\t18522\t20.000000\n", "scaffold7_cov100\t24494\t24496\t28.571429\n", "scaffold7_cov100\t24895\t24897\t38.888889\n", "scaffold7_cov100\t25157\t25159\t47.058824\n", "scaffold7_cov100\t27904\t27906\t20.000000\n", "scaffold7_cov100\t27980\t27982\t20.000000\n", "scaffold7_cov100\t28393\t28395\t14.285714\n", "scaffold7_cov100\t28420\t28422\t16.666667\n", "\n", "==> Meth2_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-paFlanksDownstream <==\n", "scaffold6_cov64\t6690\t6692\t0.000000\n", "scaffold6_cov64\t6704\t6706\t0.000000\n", "scaffold6_cov64\t6732\t6734\t0.000000\n", "scaffold6_cov64\t6751\t6753\t0.000000\n", "scaffold6_cov64\t6805\t6807\t0.000000\n", "scaffold6_cov64\t6813\t6815\t5.263158\n", "scaffold6_cov64\t6862\t6864\t0.000000\n", "scaffold6_cov64\t6880\t6882\t0.000000\n", "scaffold6_cov64\t6885\t6887\t0.000000\n", "scaffold6_cov64\t6909\t6911\t10.000000\n", "\n", "==> Meth2_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-paFlanksDownstream <==\n", "scaffold6_cov64\t6690\t6692\t0.000000\n", "scaffold6_cov64\t6704\t6706\t0.000000\n", "scaffold6_cov64\t6732\t6734\t0.000000\n", "scaffold6_cov64\t6751\t6753\t0.000000\n", "scaffold6_cov64\t6805\t6807\t0.000000\n", "scaffold6_cov64\t6813\t6815\t5.263158\n", "scaffold6_cov64\t6862\t6864\t0.000000\n", "scaffold6_cov64\t6880\t6882\t0.000000\n", "scaffold6_cov64\t6885\t6887\t0.000000\n", "scaffold6_cov64\t6909\t6911\t10.000000\n", "\n", "==> Meth3_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-paFlanksDownstream <==\n", "scaffold7_cov100\t6231\t6233\t100.000000\n", "scaffold7_cov100\t6233\t6235\t100.000000\n", "scaffold7_cov100\t18520\t18522\t66.666667\n", "scaffold7_cov100\t19284\t19286\t80.000000\n", "scaffold7_cov100\t19296\t19298\t88.888889\n", "scaffold7_cov100\t24401\t24403\t100.000000\n", "scaffold7_cov100\t24454\t24456\t66.666667\n", "scaffold7_cov100\t24509\t24511\t100.000000\n", "scaffold7_cov100\t24617\t24619\t61.538462\n", "scaffold7_cov100\t24769\t24771\t57.142857\n", "\n", "==> Meth3_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-paFlanksDownstream <==\n", "scaffold6_cov64\t6732\t6734\t14.285714\n", "scaffold7_cov100\t2708\t2710\t11.111111\n", "scaffold7_cov100\t3297\t3299\t12.500000\n", "scaffold7_cov100\t13275\t13277\t22.222222\n", "scaffold7_cov100\t24494\t24496\t22.222222\n", "scaffold7_cov100\t24557\t24559\t28.571429\n", "scaffold7_cov100\t24614\t24616\t23.076923\n", "scaffold7_cov100\t24969\t24971\t12.500000\n", "scaffold7_cov100\t25157\t25159\t23.529412\n", "scaffold7_cov100\t27596\t27598\t14.285714\n", "\n", "==> Meth3_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-paFlanksDownstream <==\n", "scaffold6_cov64\t6690\t6692\t0.000000\n", "scaffold6_cov64\t6704\t6706\t0.000000\n", "scaffold6_cov64\t6751\t6753\t0.000000\n", "scaffold6_cov64\t6805\t6807\t0.000000\n", "scaffold6_cov64\t6813\t6815\t3.571429\n", "scaffold6_cov64\t6862\t6864\t4.000000\n", "scaffold6_cov64\t6880\t6882\t0.000000\n", "scaffold6_cov64\t6885\t6887\t0.000000\n", "scaffold6_cov64\t6909\t6911\t0.000000\n", "scaffold6_cov64\t6943\t6945\t0.000000\n", "\n", "==> Meth3_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-paFlanksDownstream <==\n", "scaffold6_cov64\t6690\t6692\t0.000000\n", "scaffold6_cov64\t6704\t6706\t0.000000\n", "scaffold6_cov64\t6732\t6734\t14.285714\n", "scaffold6_cov64\t6751\t6753\t0.000000\n", "scaffold6_cov64\t6805\t6807\t0.000000\n", "scaffold6_cov64\t6813\t6815\t3.571429\n", "scaffold6_cov64\t6862\t6864\t4.000000\n", "scaffold6_cov64\t6880\t6882\t0.000000\n", "scaffold6_cov64\t6885\t6887\t0.000000\n", "scaffold6_cov64\t6909\t6911\t0.000000\n", "\n", "==> Meth4_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-paFlanksDownstream <==\n", "scaffold7_cov100\t24509\t24511\t100.000000\n", "scaffold7_cov100\t24557\t24559\t100.000000\n", "scaffold7_cov100\t384784\t384786\t50.000000\n", "scaffold7_cov100\t443190\t443192\t100.000000\n", "scaffold7_cov100\t443210\t443212\t100.000000\n", "scaffold7_cov100\t450123\t450125\t100.000000\n", "scaffold20_cov103\t75606\t75608\t50.000000\n", "scaffold28_cov97\t32052\t32054\t62.500000\n", "scaffold28_cov97\t32086\t32088\t100.000000\n", "scaffold28_cov97\t32097\t32099\t100.000000\n", "\n", "==> Meth4_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-paFlanksDownstream <==\n", "scaffold6_cov64\t6732\t6734\t16.666667\n", "scaffold7_cov100\t64192\t64194\t23.076923\n", "scaffold7_cov100\t64288\t64290\t20.000000\n", "scaffold7_cov100\t64290\t64292\t26.666667\n", "scaffold7_cov100\t116515\t116517\t30.000000\n", "scaffold7_cov100\t131326\t131328\t16.666667\n", "scaffold7_cov100\t205249\t205251\t20.000000\n", "scaffold7_cov100\t218601\t218603\t13.483146\n", "scaffold7_cov100\t257184\t257186\t20.000000\n", "scaffold7_cov100\t282741\t282743\t25.000000\n", "\n", "==> Meth4_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-paFlanksDownstream <==\n", "scaffold6_cov64\t6687\t6689\t6.666667\n", "scaffold6_cov64\t6690\t6692\t0.000000\n", "scaffold6_cov64\t6704\t6706\t2.702703\n", "scaffold6_cov64\t6751\t6753\t8.000000\n", "scaffold6_cov64\t6805\t6807\t0.000000\n", "scaffold6_cov64\t6813\t6815\t0.000000\n", "scaffold6_cov64\t6862\t6864\t0.000000\n", "scaffold6_cov64\t6880\t6882\t0.000000\n", "scaffold6_cov64\t6885\t6887\t0.000000\n", "scaffold6_cov64\t6909\t6911\t0.000000\n", "\n", "==> Meth4_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-paFlanksDownstream <==\n", "scaffold6_cov64\t6687\t6689\t6.666667\n", "scaffold6_cov64\t6690\t6692\t0.000000\n", "scaffold6_cov64\t6704\t6706\t2.702703\n", "scaffold6_cov64\t6732\t6734\t16.666667\n", "scaffold6_cov64\t6751\t6753\t8.000000\n", "scaffold6_cov64\t6805\t6807\t0.000000\n", "scaffold6_cov64\t6813\t6815\t0.000000\n", "scaffold6_cov64\t6862\t6864\t0.000000\n", "scaffold6_cov64\t6880\t6882\t0.000000\n", "scaffold6_cov64\t6885\t6887\t0.000000\n", "\n", "==> Meth5_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-paFlanksDownstream <==\n", "scaffold7_cov100\t24454\t24456\t100.000000\n", "scaffold7_cov100\t24494\t24496\t87.500000\n", "scaffold7_cov100\t24509\t24511\t100.000000\n", "scaffold7_cov100\t24557\t24559\t100.000000\n", "scaffold7_cov100\t92029\t92031\t100.000000\n", "scaffold7_cov100\t281483\t281485\t60.000000\n", "scaffold7_cov100\t281501\t281503\t60.000000\n", "scaffold7_cov100\t373659\t373661\t100.000000\n", "scaffold7_cov100\t384726\t384728\t60.000000\n", "scaffold7_cov100\t384729\t384731\t60.000000\n", "\n", "==> Meth5_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-paFlanksDownstream <==\n", "scaffold7_cov100\t24443\t24445\t16.666667\n", "scaffold7_cov100\t91999\t92001\t14.285714\n", "scaffold7_cov100\t116515\t116517\t20.000000\n", "scaffold7_cov100\t131309\t131311\t11.764706\n", "scaffold7_cov100\t210084\t210086\t22.222222\n", "scaffold7_cov100\t218601\t218603\t10.655738\n", "scaffold7_cov100\t344976\t344978\t22.222222\n", "scaffold7_cov100\t384919\t384921\t20.000000\n", "scaffold7_cov100\t498205\t498207\t13.636364\n", "scaffold19_cov103\t2571\t2573\t20.000000\n", "\n", "==> Meth5_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-paFlanksDownstream <==\n", "scaffold6_cov64\t6687\t6689\t0.000000\n", "scaffold6_cov64\t6690\t6692\t0.000000\n", "scaffold6_cov64\t6704\t6706\t0.000000\n", "scaffold6_cov64\t6751\t6753\t0.000000\n", "scaffold6_cov64\t6805\t6807\t0.000000\n", "scaffold6_cov64\t6813\t6815\t0.000000\n", "scaffold7_cov100\t3150\t3152\t5.004634\n", "scaffold7_cov100\t3194\t3196\t0.587988\n", "scaffold7_cov100\t3240\t3242\t0.420345\n", "scaffold7_cov100\t3294\t3296\t0.334588\n", "\n", "==> Meth5_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-paFlanksDownstream <==\n", "scaffold6_cov64\t6687\t6689\t0.000000\n", "scaffold6_cov64\t6690\t6692\t0.000000\n", "scaffold6_cov64\t6704\t6706\t0.000000\n", "scaffold6_cov64\t6751\t6753\t0.000000\n", "scaffold6_cov64\t6805\t6807\t0.000000\n", "scaffold6_cov64\t6813\t6815\t0.000000\n", "scaffold7_cov100\t3150\t3152\t5.004634\n", "scaffold7_cov100\t3194\t3196\t0.587988\n", "scaffold7_cov100\t3240\t3242\t0.420345\n", "scaffold7_cov100\t3294\t3296\t0.334588\n", "\n", "==> Meth6_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-paFlanksDownstream <==\n", "scaffold7_cov100\t210167\t210169\t83.333333\n", "scaffold7_cov100\t281483\t281485\t50.000000\n", "scaffold7_cov100\t281501\t281503\t55.555556\n", "scaffold7_cov100\t443190\t443192\t100.000000\n", "scaffold12_cov67\t28089\t28091\t100.000000\n", "scaffold28_cov97\t4748\t4750\t71.428571\n", "scaffold28_cov97\t4902\t4904\t71.428571\n", "scaffold42_cov106\t38134\t38136\t60.000000\n", "scaffold42_cov106\t192068\t192070\t100.000000\n", "scaffold45_cov106\t118244\t118246\t100.000000\n", "\n", "==> Meth6_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-paFlanksDownstream <==\n", "scaffold6_cov64\t6687\t6689\t14.285714\n", "scaffold6_cov64\t6704\t6706\t14.285714\n", "scaffold6_cov64\t7373\t7375\t16.666667\n", "scaffold7_cov100\t28086\t28088\t16.666667\n", "scaffold7_cov100\t131309\t131311\t20.000000\n", "scaffold7_cov100\t169073\t169075\t37.500000\n", "scaffold7_cov100\t257330\t257332\t12.500000\n", "scaffold7_cov100\t282891\t282893\t11.904762\n", "scaffold7_cov100\t340915\t340917\t28.571429\n", "scaffold7_cov100\t373659\t373661\t20.000000\n", "\n", "==> Meth6_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-paFlanksDownstream <==\n", "scaffold6_cov64\t6690\t6692\t0.000000\n", "scaffold6_cov64\t6732\t6734\t0.000000\n", "scaffold6_cov64\t6751\t6753\t0.000000\n", "scaffold6_cov64\t6805\t6807\t0.000000\n", "scaffold6_cov64\t6813\t6815\t0.000000\n", "scaffold6_cov64\t6862\t6864\t0.000000\n", "scaffold6_cov64\t6880\t6882\t0.000000\n", "scaffold6_cov64\t7263\t7265\t0.000000\n", "scaffold6_cov64\t7271\t7273\t0.000000\n", "scaffold6_cov64\t7316\t7318\t0.000000\n", "\n", "==> Meth6_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-paFlanksDownstream <==\n", "scaffold6_cov64\t6687\t6689\t14.285714\n", "scaffold6_cov64\t6690\t6692\t0.000000\n", "scaffold6_cov64\t6704\t6706\t14.285714\n", "scaffold6_cov64\t6732\t6734\t0.000000\n", "scaffold6_cov64\t6751\t6753\t0.000000\n", "scaffold6_cov64\t6805\t6807\t0.000000\n", "scaffold6_cov64\t6813\t6815\t0.000000\n", "scaffold6_cov64\t6862\t6864\t0.000000\n", "scaffold6_cov64\t6880\t6882\t0.000000\n", "scaffold6_cov64\t7263\t7265\t0.000000\n", "\n", "==> Meth7_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-paFlanksDownstream <==\n", "scaffold7_cov100\t6231\t6233\t97.142857\n", "scaffold7_cov100\t6233\t6235\t97.222222\n", "scaffold7_cov100\t12652\t12654\t81.818182\n", "scaffold7_cov100\t12662\t12664\t80.000000\n", "scaffold7_cov100\t12675\t12677\t82.608696\n", "scaffold7_cov100\t12683\t12685\t91.304348\n", "scaffold7_cov100\t12704\t12706\t76.470588\n", "scaffold7_cov100\t12726\t12728\t78.571429\n", "scaffold7_cov100\t12737\t12739\t78.571429\n", "scaffold7_cov100\t12806\t12808\t90.909091\n", "\n", "==> Meth7_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-paFlanksDownstream <==\n", "scaffold6_cov64\t6805\t6807\t14.285714\n", "scaffold6_cov64\t6880\t6882\t14.285714\n", "scaffold6_cov64\t7609\t7611\t14.285714\n", "scaffold7_cov100\t12821\t12823\t36.363636\n", "scaffold7_cov100\t12861\t12863\t40.000000\n", "scaffold7_cov100\t24614\t24616\t42.857143\n", "scaffold7_cov100\t24617\t24619\t14.285714\n", "scaffold7_cov100\t24690\t24692\t20.000000\n", "scaffold7_cov100\t24969\t24971\t20.000000\n", "scaffold7_cov100\t25157\t25159\t21.739130\n", "\n", "==> Meth7_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-paFlanksDownstream <==\n", "scaffold6_cov64\t6813\t6815\t0.000000\n", "scaffold6_cov64\t6862\t6864\t0.000000\n", "scaffold6_cov64\t6885\t6887\t0.000000\n", "scaffold6_cov64\t7097\t7099\t0.000000\n", "scaffold6_cov64\t7159\t7161\t0.000000\n", "scaffold6_cov64\t7163\t7165\t0.000000\n", "scaffold6_cov64\t7165\t7167\t0.000000\n", "scaffold6_cov64\t7177\t7179\t0.000000\n", "scaffold6_cov64\t7181\t7183\t0.000000\n", "scaffold6_cov64\t7185\t7187\t0.000000\n", "\n", "==> Meth7_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-paFlanksDownstream <==\n", "scaffold6_cov64\t6805\t6807\t14.285714\n", "scaffold6_cov64\t6813\t6815\t0.000000\n", "scaffold6_cov64\t6862\t6864\t0.000000\n", "scaffold6_cov64\t6880\t6882\t14.285714\n", "scaffold6_cov64\t6885\t6887\t0.000000\n", "scaffold6_cov64\t7097\t7099\t0.000000\n", "scaffold6_cov64\t7159\t7161\t0.000000\n", "scaffold6_cov64\t7163\t7165\t0.000000\n", "scaffold6_cov64\t7165\t7167\t0.000000\n", "scaffold6_cov64\t7177\t7179\t0.000000\n", "\n", "==> Meth8_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-paFlanksDownstream <==\n", "scaffold7_cov100\t6233\t6235\t93.103448\n", "scaffold7_cov100\t12652\t12654\t96.226415\n", "scaffold7_cov100\t12662\t12664\t92.079208\n", "scaffold7_cov100\t12675\t12677\t92.307692\n", "scaffold7_cov100\t12683\t12685\t92.134831\n", "scaffold7_cov100\t12704\t12706\t66.666667\n", "scaffold7_cov100\t12726\t12728\t59.459459\n", "scaffold7_cov100\t12737\t12739\t83.582090\n", "scaffold7_cov100\t12806\t12808\t91.176471\n", "scaffold7_cov100\t12808\t12810\t91.176471\n", "\n", "==> Meth8_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-paFlanksDownstream <==\n", "scaffold7_cov100\t6231\t6233\t42.857143\n", "scaffold7_cov100\t12861\t12863\t27.272727\n", "scaffold7_cov100\t24494\t24496\t17.647059\n", "scaffold7_cov100\t24830\t24832\t16.666667\n", "scaffold7_cov100\t24895\t24897\t20.000000\n", "scaffold7_cov100\t92019\t92021\t33.333333\n", "scaffold7_cov100\t92029\t92031\t44.444444\n", "scaffold7_cov100\t92055\t92057\t26.666667\n", "scaffold7_cov100\t92105\t92107\t41.666667\n", "scaffold7_cov100\t131300\t131302\t42.857143\n", "\n", "==> Meth8_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-paFlanksDownstream <==\n", "scaffold7_cov100\t12587\t12589\t0.840336\n", "scaffold7_cov100\t13038\t13040\t3.448276\n", "scaffold7_cov100\t24617\t24619\t0.000000\n", "scaffold7_cov100\t24690\t24692\t0.000000\n", "scaffold7_cov100\t136029\t136031\t0.000000\n", "scaffold7_cov100\t136059\t136061\t0.000000\n", "scaffold7_cov100\t196835\t196837\t0.000000\n", "scaffold7_cov100\t196933\t196935\t0.000000\n", "scaffold7_cov100\t196938\t196940\t0.000000\n", "scaffold7_cov100\t260705\t260707\t0.000000\n", "\n", "==> Meth8_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-paFlanksDownstream <==\n", "scaffold7_cov100\t6231\t6233\t42.857143\n", "scaffold7_cov100\t6233\t6235\t93.103448\n", "scaffold7_cov100\t12587\t12589\t0.840336\n", "scaffold7_cov100\t12652\t12654\t96.226415\n", "scaffold7_cov100\t12662\t12664\t92.079208\n", "scaffold7_cov100\t12675\t12677\t92.307692\n", "scaffold7_cov100\t12683\t12685\t92.134831\n", "scaffold7_cov100\t12704\t12706\t66.666667\n", "scaffold7_cov100\t12726\t12728\t59.459459\n", "scaffold7_cov100\t12737\t12739\t83.582090\n", "\n", "==> Meth9_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-paFlanksDownstream <==\n", "scaffold7_cov100\t6231\t6233\t95.555556\n", "scaffold7_cov100\t6233\t6235\t97.619048\n", "scaffold7_cov100\t12652\t12654\t90.909091\n", "scaffold7_cov100\t12662\t12664\t80.000000\n", "scaffold7_cov100\t12675\t12677\t80.000000\n", "scaffold7_cov100\t12704\t12706\t50.000000\n", "scaffold7_cov100\t12726\t12728\t57.142857\n", "scaffold7_cov100\t12857\t12859\t60.000000\n", "scaffold7_cov100\t19284\t19286\t94.318182\n", "scaffold7_cov100\t19296\t19298\t97.530864\n", "\n", "==> Meth9_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-paFlanksDownstream <==\n", "scaffold7_cov100\t12587\t12589\t12.500000\n", "scaffold7_cov100\t12683\t12685\t40.000000\n", "scaffold7_cov100\t12737\t12739\t28.571429\n", "scaffold7_cov100\t12821\t12823\t42.857143\n", "scaffold7_cov100\t12861\t12863\t20.000000\n", "scaffold7_cov100\t13275\t13277\t47.619048\n", "scaffold7_cov100\t24614\t24616\t47.619048\n", "scaffold7_cov100\t24617\t24619\t42.857143\n", "scaffold7_cov100\t25157\t25159\t42.857143\n", "scaffold7_cov100\t78244\t78246\t20.000000\n", "\n", "==> Meth9_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-paFlanksDownstream <==\n", "scaffold6_cov64\t6751\t6753\t0.000000\n", "scaffold6_cov64\t6805\t6807\t0.000000\n", "scaffold6_cov64\t6813\t6815\t0.000000\n", "scaffold6_cov64\t6862\t6864\t0.000000\n", "scaffold6_cov64\t6880\t6882\t7.142857\n", "scaffold6_cov64\t6885\t6887\t0.000000\n", "scaffold6_cov64\t6909\t6911\t0.000000\n", "scaffold6_cov64\t6943\t6945\t0.000000\n", "scaffold6_cov64\t6991\t6993\t0.000000\n", "scaffold6_cov64\t7011\t7013\t0.000000\n", "\n", "==> Meth9_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-paFlanksDownstream <==\n", "scaffold6_cov64\t6751\t6753\t0.000000\n", "scaffold6_cov64\t6805\t6807\t0.000000\n", "scaffold6_cov64\t6813\t6815\t0.000000\n", "scaffold6_cov64\t6862\t6864\t0.000000\n", "scaffold6_cov64\t6880\t6882\t7.142857\n", "scaffold6_cov64\t6885\t6887\t0.000000\n", "scaffold6_cov64\t6909\t6911\t0.000000\n", "scaffold6_cov64\t6943\t6945\t0.000000\n", "scaffold6_cov64\t6991\t6993\t0.000000\n", "scaffold6_cov64\t7011\t7013\t0.000000\n" ] } ], "source": [ "#Check output\n", "!head *paFlanksDownstream" ] }, { "cell_type": "code", "execution_count": 213, "metadata": { "collapsed": false, "scrolled": true }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ " 13174 Meth1_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-paFlanksDownstream\n", " 41423 Meth1_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-paFlanksDownstream\n", " 538748 Meth1_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-paFlanksDownstream\n", " 593345 Meth1_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-paFlanksDownstream\n", " 15359 Meth2_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-paFlanksDownstream\n", " 40530 Meth2_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-paFlanksDownstream\n", " 630948 Meth2_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-paFlanksDownstream\n", " 686837 Meth2_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-paFlanksDownstream\n", " 14934 Meth3_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-paFlanksDownstream\n", " 43793 Meth3_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-paFlanksDownstream\n", " 569790 Meth3_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-paFlanksDownstream\n", " 628517 Meth3_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-paFlanksDownstream\n", " 3253 Meth4_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-paFlanksDownstream\n", " 13907 Meth4_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-paFlanksDownstream\n", " 169277 Meth4_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-paFlanksDownstream\n", " 186437 Meth4_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-paFlanksDownstream\n", " 3061 Meth5_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-paFlanksDownstream\n", " 6540 Meth5_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-paFlanksDownstream\n", " 138077 Meth5_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-paFlanksDownstream\n", " 147678 Meth5_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-paFlanksDownstream\n", " 2660 Meth6_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-paFlanksDownstream\n", " 8817 Meth6_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-paFlanksDownstream\n", " 142856 Meth6_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-paFlanksDownstream\n", " 154333 Meth6_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-paFlanksDownstream\n", " 27785 Meth7_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-paFlanksDownstream\n", " 29904 Meth7_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-paFlanksDownstream\n", " 193571 Meth7_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-paFlanksDownstream\n", " 251260 Meth7_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-paFlanksDownstream\n", " 22171 Meth8_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-paFlanksDownstream\n", " 7677 Meth8_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-paFlanksDownstream\n", " 19030 Meth8_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-paFlanksDownstream\n", " 48878 Meth8_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-paFlanksDownstream\n", " 28375 Meth9_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-paFlanksDownstream\n", " 34209 Meth9_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-paFlanksDownstream\n", " 204309 Meth9_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-paFlanksDownstream\n", " 266893 Meth9_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-paFlanksDownstream\n", " 5928356 total\n" ] } ], "source": [ "#Count number of overlaps\n", "!wc -l *paFlanksDownstream" ] }, { "cell_type": "code", "execution_count": 214, "metadata": { "collapsed": true }, "outputs": [], "source": [ "!wc -l *paFlanksDownstream > Pact-5x-paFlanksDownstream-counts.txt" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "#### 4h. Intergenic" ] }, { "cell_type": "code", "execution_count": 215, "metadata": { "collapsed": true }, "outputs": [], "source": [ "%%bash \n", "\n", "for f in *bed\n", "do\n", " /usr/local/bin/intersectBed \\\n", " -u \\\n", " -a ${f} \\\n", " -b ../../../genome-feature-files/Pact.GFFannotation.intergenic.bed \\\n", " > ${f}-paIntergenic\n", "done" ] }, { "cell_type": "code", "execution_count": 216, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "==> Meth1_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-paIntergenic <==\n", "scaffold7_cov100\t230214\t230216\t100.000000\n", "scaffold7_cov100\t230317\t230319\t54.545455\n", "scaffold7_cov100\t230584\t230586\t71.428571\n", "scaffold7_cov100\t273435\t273437\t100.000000\n", "scaffold7_cov100\t326521\t326523\t71.428571\n", "scaffold7_cov100\t371129\t371131\t66.666667\n", "scaffold7_cov100\t507795\t507797\t55.555556\n", "scaffold7_cov100\t508171\t508173\t66.666667\n", "scaffold19_cov103\t23991\t23993\t81.818182\n", "scaffold19_cov103\t24166\t24168\t88.888889\n", "\n", "==> Meth1_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-paIntergenic <==\n", "scaffold1_cov55\t102\t104\t16.666667\n", "scaffold1_cov55\t186\t188\t20.000000\n", "scaffold3_cov83\t118\t120\t12.500000\n", "scaffold3_cov83\t137\t139\t12.500000\n", "scaffold3_cov83\t475\t477\t18.750000\n", "scaffold3_cov83\t484\t486\t14.893617\n", "scaffold3_cov83\t504\t506\t21.052632\n", "scaffold6_cov64\t7983\t7985\t11.111111\n", "scaffold7_cov100\t26915\t26917\t20.000000\n", "scaffold7_cov100\t27146\t27148\t11.111111\n", "\n", "==> Meth1_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-paIntergenic <==\n", "scaffold1_cov55\t105\t107\t0.000000\n", "scaffold1_cov55\t116\t118\t0.000000\n", "scaffold1_cov55\t119\t121\t0.000000\n", "scaffold1_cov55\t146\t148\t0.000000\n", "scaffold1_cov55\t194\t196\t0.000000\n", "scaffold2_cov51\t649\t651\t0.000000\n", "scaffold2_cov51\t686\t688\t8.333333\n", "scaffold2_cov51\t778\t780\t0.000000\n", "scaffold3_cov83\t130\t132\t0.000000\n", "scaffold3_cov83\t189\t191\t6.250000\n", "\n", "==> Meth1_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-paIntergenic <==\n", "scaffold1_cov55\t102\t104\t16.666667\n", "scaffold1_cov55\t105\t107\t0.000000\n", "scaffold1_cov55\t116\t118\t0.000000\n", "scaffold1_cov55\t119\t121\t0.000000\n", "scaffold1_cov55\t146\t148\t0.000000\n", "scaffold1_cov55\t186\t188\t20.000000\n", "scaffold1_cov55\t194\t196\t0.000000\n", "scaffold2_cov51\t649\t651\t0.000000\n", "scaffold2_cov51\t686\t688\t8.333333\n", "scaffold2_cov51\t778\t780\t0.000000\n", "\n", "==> Meth2_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-paIntergenic <==\n", "scaffold7_cov100\t230214\t230216\t85.714286\n", "scaffold7_cov100\t230584\t230586\t80.000000\n", "scaffold7_cov100\t265128\t265130\t50.000000\n", "scaffold7_cov100\t265783\t265785\t70.000000\n", "scaffold7_cov100\t273435\t273437\t50.000000\n", "scaffold7_cov100\t304601\t304603\t57.142857\n", "scaffold7_cov100\t326521\t326523\t80.000000\n", "scaffold7_cov100\t372118\t372120\t66.666667\n", "scaffold7_cov100\t457456\t457458\t60.000000\n", "scaffold19_cov103\t23991\t23993\t93.333333\n", "\n", "==> Meth2_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-paIntergenic <==\n", "scaffold1_cov55\t105\t107\t12.500000\n", "scaffold1_cov55\t252\t254\t20.000000\n", "scaffold2_cov51\t686\t688\t11.111111\n", "scaffold7_cov100\t39381\t39383\t16.666667\n", "scaffold7_cov100\t84872\t84874\t16.666667\n", "scaffold7_cov100\t84995\t84997\t16.666667\n", "scaffold7_cov100\t85393\t85395\t14.285714\n", "scaffold7_cov100\t85442\t85444\t14.285714\n", "scaffold7_cov100\t103614\t103616\t12.500000\n", "scaffold7_cov100\t104699\t104701\t11.111111\n", "\n", "==> Meth2_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-paIntergenic <==\n", "scaffold1_cov55\t49\t51\t0.000000\n", "scaffold1_cov55\t84\t86\t0.000000\n", "scaffold1_cov55\t92\t94\t0.000000\n", "scaffold1_cov55\t102\t104\t0.000000\n", "scaffold1_cov55\t116\t118\t0.000000\n", "scaffold1_cov55\t119\t121\t0.000000\n", "scaffold1_cov55\t146\t148\t0.000000\n", "scaffold1_cov55\t169\t171\t0.000000\n", "scaffold1_cov55\t186\t188\t0.000000\n", "scaffold1_cov55\t194\t196\t0.000000\n", "\n", "==> Meth2_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-paIntergenic <==\n", "scaffold1_cov55\t49\t51\t0.000000\n", "scaffold1_cov55\t84\t86\t0.000000\n", "scaffold1_cov55\t92\t94\t0.000000\n", "scaffold1_cov55\t102\t104\t0.000000\n", "scaffold1_cov55\t105\t107\t12.500000\n", "scaffold1_cov55\t116\t118\t0.000000\n", "scaffold1_cov55\t119\t121\t0.000000\n", "scaffold1_cov55\t146\t148\t0.000000\n", "scaffold1_cov55\t169\t171\t0.000000\n", "scaffold1_cov55\t186\t188\t0.000000\n", "\n", "==> Meth3_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-paIntergenic <==\n", "scaffold7_cov100\t230214\t230216\t66.666667\n", "scaffold7_cov100\t230584\t230586\t91.666667\n", "scaffold7_cov100\t267338\t267340\t54.545455\n", "scaffold7_cov100\t267366\t267368\t50.000000\n", "scaffold7_cov100\t273435\t273437\t75.000000\n", "scaffold7_cov100\t326521\t326523\t100.000000\n", "scaffold7_cov100\t457255\t457257\t69.230769\n", "scaffold7_cov100\t507824\t507826\t50.000000\n", "scaffold19_cov103\t23991\t23993\t92.857143\n", "scaffold19_cov103\t24166\t24168\t75.000000\n", "\n", "==> Meth3_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-paIntergenic <==\n", "scaffold1_cov55\t119\t121\t20.000000\n", "scaffold1_cov55\t194\t196\t20.000000\n", "scaffold2_cov51\t686\t688\t15.384615\n", "scaffold3_cov83\t189\t191\t14.285714\n", "scaffold3_cov83\t475\t477\t13.333333\n", "scaffold7_cov100\t39178\t39180\t16.666667\n", "scaffold7_cov100\t40148\t40150\t14.285714\n", "scaffold7_cov100\t83934\t83936\t16.666667\n", "scaffold7_cov100\t84083\t84085\t25.000000\n", "scaffold7_cov100\t84259\t84261\t14.285714\n", "\n", "==> Meth3_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-paIntergenic <==\n", "scaffold1_cov55\t250\t252\t0.000000\n", "scaffold2_cov51\t649\t651\t0.000000\n", "scaffold2_cov51\t778\t780\t0.000000\n", "scaffold3_cov83\t118\t120\t0.000000\n", "scaffold3_cov83\t130\t132\t0.000000\n", "scaffold3_cov83\t137\t139\t0.000000\n", "scaffold3_cov83\t208\t210\t5.128205\n", "scaffold3_cov83\t243\t245\t2.272727\n", "scaffold3_cov83\t261\t263\t6.666667\n", "scaffold3_cov83\t484\t486\t4.444444\n", "\n", "==> Meth3_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-paIntergenic <==\n", "scaffold1_cov55\t119\t121\t20.000000\n", "scaffold1_cov55\t194\t196\t20.000000\n", "scaffold1_cov55\t250\t252\t0.000000\n", "scaffold2_cov51\t649\t651\t0.000000\n", "scaffold2_cov51\t686\t688\t15.384615\n", "scaffold2_cov51\t778\t780\t0.000000\n", "scaffold3_cov83\t118\t120\t0.000000\n", "scaffold3_cov83\t130\t132\t0.000000\n", "scaffold3_cov83\t137\t139\t0.000000\n", "scaffold3_cov83\t189\t191\t14.285714\n", "\n", "==> Meth4_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-paIntergenic <==\n", "scaffold7_cov100\t84631\t84633\t62.500000\n", "scaffold7_cov100\t165239\t165241\t100.000000\n", "scaffold7_cov100\t228104\t228106\t100.000000\n", "scaffold7_cov100\t233612\t233614\t66.666667\n", "scaffold7_cov100\t265131\t265133\t50.000000\n", "scaffold7_cov100\t478999\t479001\t50.000000\n", "scaffold7_cov100\t507795\t507797\t100.000000\n", "scaffold7_cov100\t507816\t507818\t85.714286\n", "scaffold7_cov100\t507824\t507826\t66.666667\n", "scaffold7_cov100\t507973\t507975\t55.555556\n", "\n", "==> Meth4_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-paIntergenic <==\n", "scaffold7_cov100\t39365\t39367\t25.000000\n", "scaffold7_cov100\t39367\t39369\t25.000000\n", "scaffold7_cov100\t40132\t40134\t26.666667\n", "scaffold7_cov100\t40148\t40150\t21.052632\n", "scaffold7_cov100\t85669\t85671\t18.181818\n", "scaffold7_cov100\t86732\t86734\t37.500000\n", "scaffold7_cov100\t86745\t86747\t42.857143\n", "scaffold7_cov100\t193152\t193154\t42.857143\n", "scaffold7_cov100\t214755\t214757\t16.666667\n", "scaffold7_cov100\t221703\t221705\t33.333333\n", "\n", "==> Meth4_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-paIntergenic <==\n", "scaffold6_cov64\t7952\t7954\t0.000000\n", "scaffold6_cov64\t7983\t7985\t0.000000\n", "scaffold6_cov64\t8041\t8043\t0.000000\n", "scaffold6_cov64\t8056\t8058\t0.000000\n", "scaffold6_cov64\t8070\t8072\t0.000000\n", "scaffold6_cov64\t8079\t8081\t0.000000\n", "scaffold7_cov100\t27507\t27509\t0.000000\n", "scaffold7_cov100\t39104\t39106\t0.000000\n", "scaffold7_cov100\t39113\t39115\t0.000000\n", "scaffold7_cov100\t39169\t39171\t0.000000\n", "\n", "==> Meth4_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-paIntergenic <==\n", "scaffold6_cov64\t7952\t7954\t0.000000\n", "scaffold6_cov64\t7983\t7985\t0.000000\n", "scaffold6_cov64\t8041\t8043\t0.000000\n", "scaffold6_cov64\t8056\t8058\t0.000000\n", "scaffold6_cov64\t8070\t8072\t0.000000\n", "scaffold6_cov64\t8079\t8081\t0.000000\n", "scaffold7_cov100\t27507\t27509\t0.000000\n", "scaffold7_cov100\t39104\t39106\t0.000000\n", "scaffold7_cov100\t39113\t39115\t0.000000\n", "scaffold7_cov100\t39169\t39171\t0.000000\n", "\n", "==> Meth5_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-paIntergenic <==\n", "scaffold7_cov100\t165090\t165092\t100.000000\n", "scaffold7_cov100\t165239\t165241\t100.000000\n", "scaffold7_cov100\t193152\t193154\t55.555556\n", "scaffold7_cov100\t223753\t223755\t100.000000\n", "scaffold7_cov100\t255876\t255878\t50.000000\n", "scaffold7_cov100\t265811\t265813\t80.000000\n", "scaffold19_cov103\t35674\t35676\t100.000000\n", "scaffold19_cov103\t204082\t204084\t57.894737\n", "scaffold19_cov103\t226455\t226457\t50.000000\n", "scaffold19_cov103\t239859\t239861\t53.846154\n", "\n", "==> Meth5_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-paIntergenic <==\n", "scaffold7_cov100\t103351\t103353\t11.111111\n", "scaffold7_cov100\t191986\t191988\t18.181818\n", "scaffold7_cov100\t195511\t195513\t14.285714\n", "scaffold7_cov100\t240751\t240753\t33.333333\n", "scaffold7_cov100\t242339\t242341\t16.666667\n", "scaffold7_cov100\t255879\t255881\t40.000000\n", "scaffold7_cov100\t256583\t256585\t16.666667\n", "scaffold7_cov100\t398842\t398844\t16.666667\n", "scaffold7_cov100\t479282\t479284\t16.666667\n", "scaffold7_cov100\t479805\t479807\t14.285714\n", "\n", "==> Meth5_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-paIntergenic <==\n", "scaffold7_cov100\t26273\t26275\t0.000000\n", "scaffold7_cov100\t27357\t27359\t0.000000\n", "scaffold7_cov100\t27380\t27382\t0.000000\n", "scaffold7_cov100\t27385\t27387\t0.000000\n", "scaffold7_cov100\t27507\t27509\t0.000000\n", "scaffold7_cov100\t39992\t39994\t0.000000\n", "scaffold7_cov100\t40014\t40016\t0.000000\n", "scaffold7_cov100\t40049\t40051\t0.000000\n", "scaffold7_cov100\t40077\t40079\t0.000000\n", "scaffold7_cov100\t40132\t40134\t0.000000\n", "\n", "==> Meth5_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-paIntergenic <==\n", "scaffold7_cov100\t26273\t26275\t0.000000\n", "scaffold7_cov100\t27357\t27359\t0.000000\n", "scaffold7_cov100\t27380\t27382\t0.000000\n", "scaffold7_cov100\t27385\t27387\t0.000000\n", "scaffold7_cov100\t27507\t27509\t0.000000\n", "scaffold7_cov100\t39992\t39994\t0.000000\n", "scaffold7_cov100\t40014\t40016\t0.000000\n", "scaffold7_cov100\t40049\t40051\t0.000000\n", "scaffold7_cov100\t40077\t40079\t0.000000\n", "scaffold7_cov100\t40132\t40134\t0.000000\n", "\n", "==> Meth6_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-paIntergenic <==\n", "scaffold7_cov100\t223257\t223259\t57.142857\n", "scaffold7_cov100\t223265\t223267\t57.142857\n", "scaffold7_cov100\t223270\t223272\t57.142857\n", "scaffold7_cov100\t396871\t396873\t100.000000\n", "scaffold7_cov100\t507816\t507818\t72.549020\n", "scaffold7_cov100\t507824\t507826\t52.941176\n", "scaffold12_cov67\t29579\t29581\t60.000000\n", "scaffold14_cov75\t8988\t8990\t75.000000\n", "scaffold19_cov103\t239610\t239612\t50.000000\n", "scaffold21_cov102\t22420\t22422\t66.666667\n", "\n", "==> Meth6_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-paIntergenic <==\n", "scaffold7_cov100\t39104\t39106\t33.333333\n", "scaffold7_cov100\t39113\t39115\t33.333333\n", "scaffold7_cov100\t39169\t39171\t33.333333\n", "scaffold7_cov100\t39178\t39180\t33.333333\n", "scaffold7_cov100\t39192\t39194\t33.333333\n", "scaffold7_cov100\t164670\t164672\t12.500000\n", "scaffold7_cov100\t193614\t193616\t20.000000\n", "scaffold7_cov100\t195511\t195513\t20.000000\n", "scaffold7_cov100\t195519\t195521\t12.500000\n", "scaffold7_cov100\t223230\t223232\t28.571429\n", "\n", "==> Meth6_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-paIntergenic <==\n", "scaffold6_cov64\t7983\t7985\t0.000000\n", "scaffold6_cov64\t8041\t8043\t0.000000\n", "scaffold6_cov64\t8056\t8058\t0.000000\n", "scaffold6_cov64\t8070\t8072\t0.000000\n", "scaffold6_cov64\t8079\t8081\t0.000000\n", "scaffold7_cov100\t27507\t27509\t0.000000\n", "scaffold7_cov100\t39269\t39271\t0.000000\n", "scaffold7_cov100\t39282\t39284\t0.000000\n", "scaffold7_cov100\t40148\t40150\t0.000000\n", "scaffold7_cov100\t84236\t84238\t0.000000\n", "\n", "==> Meth6_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-paIntergenic <==\n", "scaffold6_cov64\t7983\t7985\t0.000000\n", "scaffold6_cov64\t8041\t8043\t0.000000\n", "scaffold6_cov64\t8056\t8058\t0.000000\n", "scaffold6_cov64\t8070\t8072\t0.000000\n", "scaffold6_cov64\t8079\t8081\t0.000000\n", "scaffold7_cov100\t27507\t27509\t0.000000\n", "scaffold7_cov100\t39104\t39106\t33.333333\n", "scaffold7_cov100\t39113\t39115\t33.333333\n", "scaffold7_cov100\t39169\t39171\t33.333333\n", "scaffold7_cov100\t39178\t39180\t33.333333\n", "\n", "==> Meth7_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-paIntergenic <==\n", "scaffold3_cov83\t118\t120\t60.000000\n", "scaffold3_cov83\t137\t139\t50.000000\n", "scaffold3_cov83\t261\t263\t69.444444\n", "scaffold3_cov83\t475\t477\t72.727273\n", "scaffold3_cov83\t484\t486\t64.705882\n", "scaffold3_cov83\t504\t506\t83.333333\n", "scaffold7_cov100\t216293\t216295\t60.000000\n", "scaffold7_cov100\t230584\t230586\t87.500000\n", "scaffold7_cov100\t267363\t267365\t80.000000\n", "scaffold7_cov100\t273435\t273437\t100.000000\n", "\n", "==> Meth7_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-paIntergenic <==\n", "scaffold3_cov83\t130\t132\t40.000000\n", "scaffold3_cov83\t189\t191\t44.444444\n", "scaffold3_cov83\t208\t210\t42.857143\n", "scaffold7_cov100\t86618\t86620\t20.000000\n", "scaffold7_cov100\t103856\t103858\t20.000000\n", "scaffold7_cov100\t136247\t136249\t20.000000\n", "scaffold7_cov100\t164482\t164484\t20.000000\n", "scaffold7_cov100\t189422\t189424\t20.000000\n", "scaffold7_cov100\t189915\t189917\t20.000000\n", "scaffold7_cov100\t190047\t190049\t20.000000\n", "\n", "==> Meth7_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-paIntergenic <==\n", "scaffold2_cov51\t649\t651\t0.000000\n", "scaffold2_cov51\t686\t688\t0.000000\n", "scaffold2_cov51\t778\t780\t0.000000\n", "scaffold3_cov83\t243\t245\t0.000000\n", "scaffold6_cov64\t7687\t7689\t0.000000\n", "scaffold6_cov64\t7693\t7695\t0.000000\n", "scaffold6_cov64\t7698\t7700\t0.000000\n", "scaffold6_cov64\t7701\t7703\t0.000000\n", "scaffold6_cov64\t7703\t7705\t0.000000\n", "scaffold6_cov64\t7789\t7791\t0.000000\n", "\n", "==> Meth7_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-paIntergenic <==\n", "scaffold2_cov51\t649\t651\t0.000000\n", "scaffold2_cov51\t686\t688\t0.000000\n", "scaffold2_cov51\t778\t780\t0.000000\n", "scaffold3_cov83\t118\t120\t60.000000\n", "scaffold3_cov83\t130\t132\t40.000000\n", "scaffold3_cov83\t137\t139\t50.000000\n", "scaffold3_cov83\t189\t191\t44.444444\n", "scaffold3_cov83\t208\t210\t42.857143\n", "scaffold3_cov83\t243\t245\t0.000000\n", "scaffold3_cov83\t261\t263\t69.444444\n", "\n", "==> Meth8_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-paIntergenic <==\n", "scaffold3_cov83\t208\t210\t60.000000\n", "scaffold3_cov83\t261\t263\t50.000000\n", "scaffold3_cov83\t475\t477\t63.636364\n", "scaffold7_cov100\t267189\t267191\t80.000000\n", "scaffold7_cov100\t304579\t304581\t97.368421\n", "scaffold7_cov100\t304583\t304585\t95.000000\n", "scaffold7_cov100\t304590\t304592\t89.743590\n", "scaffold7_cov100\t304601\t304603\t90.243902\n", "scaffold7_cov100\t304605\t304607\t71.794872\n", "scaffold7_cov100\t304616\t304618\t91.891892\n", "\n", "==> Meth8_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-paIntergenic <==\n", "scaffold3_cov83\t484\t486\t45.454545\n", "scaffold3_cov83\t504\t506\t20.000000\n", "scaffold7_cov100\t194583\t194585\t14.285714\n", "scaffold7_cov100\t194675\t194677\t16.666667\n", "scaffold7_cov100\t194695\t194697\t20.000000\n", "scaffold7_cov100\t266988\t266990\t40.000000\n", "scaffold7_cov100\t266999\t267001\t20.000000\n", "scaffold7_cov100\t267160\t267162\t20.000000\n", "scaffold7_cov100\t304543\t304545\t23.529412\n", "scaffold7_cov100\t304685\t304687\t35.384615\n", "\n", "==> Meth8_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-paIntergenic <==\n", "scaffold3_cov83\t243\t245\t0.000000\n", "scaffold7_cov100\t104260\t104262\t0.000000\n", "scaffold7_cov100\t104270\t104272\t0.000000\n", "scaffold7_cov100\t104322\t104324\t0.000000\n", "scaffold7_cov100\t104325\t104327\t0.000000\n", "scaffold7_cov100\t194522\t194524\t0.000000\n", "scaffold7_cov100\t194546\t194548\t0.000000\n", "scaffold7_cov100\t194562\t194564\t0.000000\n", "scaffold7_cov100\t194607\t194609\t0.000000\n", "scaffold7_cov100\t194642\t194644\t0.000000\n", "\n", "==> Meth8_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-paIntergenic <==\n", "scaffold3_cov83\t208\t210\t60.000000\n", "scaffold3_cov83\t243\t245\t0.000000\n", "scaffold3_cov83\t261\t263\t50.000000\n", "scaffold3_cov83\t475\t477\t63.636364\n", "scaffold3_cov83\t484\t486\t45.454545\n", "scaffold3_cov83\t504\t506\t20.000000\n", "scaffold7_cov100\t104260\t104262\t0.000000\n", "scaffold7_cov100\t104270\t104272\t0.000000\n", "scaffold7_cov100\t104322\t104324\t0.000000\n", "scaffold7_cov100\t104325\t104327\t0.000000\n", "\n", "==> Meth9_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-paIntergenic <==\n", "scaffold7_cov100\t230584\t230586\t83.333333\n", "scaffold7_cov100\t267160\t267162\t75.000000\n", "scaffold7_cov100\t267338\t267340\t64.705882\n", "scaffold7_cov100\t267358\t267360\t55.555556\n", "scaffold7_cov100\t267363\t267365\t77.777778\n", "scaffold7_cov100\t267366\t267368\t75.000000\n", "scaffold7_cov100\t273435\t273437\t100.000000\n", "scaffold7_cov100\t304579\t304581\t82.352941\n", "scaffold7_cov100\t304583\t304585\t82.352941\n", "scaffold7_cov100\t304590\t304592\t77.777778\n", "\n", "==> Meth9_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-paIntergenic <==\n", "scaffold3_cov83\t118\t120\t14.285714\n", "scaffold3_cov83\t130\t132\t12.500000\n", "scaffold3_cov83\t137\t139\t25.000000\n", "scaffold3_cov83\t189\t191\t38.461538\n", "scaffold3_cov83\t208\t210\t23.529412\n", "scaffold3_cov83\t261\t263\t23.809524\n", "scaffold3_cov83\t475\t477\t48.000000\n", "scaffold3_cov83\t484\t486\t32.000000\n", "scaffold7_cov100\t84212\t84214\t16.666667\n", "scaffold7_cov100\t84244\t84246\t20.000000\n", "\n", "==> Meth9_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-paIntergenic <==\n", "scaffold3_cov83\t243\t245\t0.000000\n", "scaffold6_cov64\t7789\t7791\t9.090909\n", "scaffold6_cov64\t7810\t7812\t0.000000\n", "scaffold6_cov64\t7812\t7814\t0.000000\n", "scaffold6_cov64\t7822\t7824\t0.000000\n", "scaffold6_cov64\t7830\t7832\t0.000000\n", "scaffold6_cov64\t7832\t7834\t0.000000\n", "scaffold6_cov64\t7847\t7849\t0.000000\n", "scaffold6_cov64\t7855\t7857\t0.000000\n", "scaffold6_cov64\t7866\t7868\t0.000000\n", "\n", "==> Meth9_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-paIntergenic <==\n", "scaffold3_cov83\t118\t120\t14.285714\n", "scaffold3_cov83\t130\t132\t12.500000\n", "scaffold3_cov83\t137\t139\t25.000000\n", "scaffold3_cov83\t189\t191\t38.461538\n", "scaffold3_cov83\t208\t210\t23.529412\n", "scaffold3_cov83\t243\t245\t0.000000\n", "scaffold3_cov83\t261\t263\t23.809524\n", "scaffold3_cov83\t475\t477\t48.000000\n", "scaffold3_cov83\t484\t486\t32.000000\n", "scaffold6_cov64\t7789\t7791\t9.090909\n" ] } ], "source": [ "#Check output\n", "!head *paIntergenic" ] }, { "cell_type": "code", "execution_count": 217, "metadata": { "collapsed": false, "scrolled": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ " 17320 Meth1_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-paIntergenic\n", " 136484 Meth1_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-paIntergenic\n", " 1816318 Meth1_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-paIntergenic\n", " 1970122 Meth1_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-paIntergenic\n", " 18574 Meth2_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-paIntergenic\n", " 131867 Meth2_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-paIntergenic\n", " 2167398 Meth2_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-paIntergenic\n", " 2317839 Meth2_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-paIntergenic\n", " 20691 Meth3_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-paIntergenic\n", " 147023 Meth3_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-paIntergenic\n", " 1935891 Meth3_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-paIntergenic\n", " 2103605 Meth3_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-paIntergenic\n", " 11969 Meth4_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-paIntergenic\n", " 55500 Meth4_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-paIntergenic\n", " 628931 Meth4_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-paIntergenic\n", " 696400 Meth4_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-paIntergenic\n", " 12047 Meth5_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-paIntergenic\n", " 26504 Meth5_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-paIntergenic\n", " 516926 Meth5_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-paIntergenic\n", " 555477 Meth5_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-paIntergenic\n", " 10629 Meth6_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-paIntergenic\n", " 36825 Meth6_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-paIntergenic\n", " 529826 Meth6_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-paIntergenic\n", " 577280 Meth6_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-paIntergenic\n", " 98419 Meth7_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-paIntergenic\n", " 124696 Meth7_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-paIntergenic\n", " 696362 Meth7_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-paIntergenic\n", " 919477 Meth7_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-paIntergenic\n", " 94478 Meth8_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-paIntergenic\n", " 39912 Meth8_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-paIntergenic\n", " 104665 Meth8_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-paIntergenic\n", " 239055 Meth8_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-paIntergenic\n", " 87520 Meth9_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-Meth.bed-paIntergenic\n", " 140365 Meth9_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-sparseMeth.bed-paIntergenic\n", " 727400 Meth9_R1_001_val_1_bismark_bt2_pe._5x.bedgraph-unMeth.bed-paIntergenic\n", " 955285 Meth9_R1_001_val_1_bismark_bt2_pe._5x.bedgraph.bed-paIntergenic\n", " 20669080 total\n" ] } ], "source": [ "#Count number of overlaps\n", "!wc -l *paIntergenic" ] }, { "cell_type": "code", "execution_count": 218, "metadata": { "collapsed": true }, "outputs": [], "source": [ "!wc -l *paIntergenic > Pact-5x-paIntergenic-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": 2 }