{ "cells": [ { "cell_type": "markdown", "metadata": {}, "source": [ "# Characterizing CpG Methylation (10x 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 10x 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": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "/Users/yaaminivenkataraman/Documents/Meth_Compare/scripts\r\n" ] } ], "source": [ "!pwd" ] }, { "cell_type": "code", "execution_count": 2, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "/Users/yaaminivenkataraman/Documents/Meth_Compare/analyses\n" ] } ], "source": [ "cd ../analyses/" ] }, { "cell_type": "code", "execution_count": 3, "metadata": { "collapsed": true }, "outputs": [], "source": [ "#!mkdir Characterizing-CpG-Methylation" ] }, { "cell_type": "code", "execution_count": 3, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "/Users/yaaminivenkataraman/Documents/Meth_Compare/analyses/Characterizing-CpG-Methylation\n" ] } ], "source": [ "cd Characterizing-CpG-Methylation/" ] }, { "cell_type": "code", "execution_count": 4, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "--2020-04-27 20:39:02-- https://gannet.fish.washington.edu/metacarcinus/FROGER_meth_compare/20200410/all_031520-TG-bs_files_GANNET_md5sum.txt\n", "Resolving gannet.fish.washington.edu... 128.95.149.52\n", "Connecting to 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’\n", "\n", "all_031520-TG-bs_fi 100%[===================>] 88.29K 241KB/s in 0.4s \n", "\n", "2020-04-27 20:39:03 (241 KB/s) - ‘all_031520-TG-bs_files_GANNET_md5sum.txt’ 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": 5, "metadata": {}, "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": 6, "metadata": {}, "outputs": [], "source": [ "#Get all lines from original checksum document\n", "#Extract information for 10x 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 10x.bedgraph \\\n", "| grep Mcap \\\n", "| cut -c1-32 \\\n", "> Mcap-10xbedgraph-GANNET-md5sum-hashes.txt" ] }, { "cell_type": "code", "execution_count": 7, "metadata": {}, "outputs": [], "source": [ "#Get all lines from original checksum document\n", "#Extract information for 10x 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 10x.bedgraph \\\n", "| grep Mcap \\\n", "| rev \\\n", "| cut -c1-48 \\\n", "| rev \\\n", "> Mcap-10xbedgraph-GANNET-md5sum-paths.txt" ] }, { "cell_type": "code", "execution_count": 8, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "4bdfd534665f8cd4cfbe29253999a630\tMeth10_R1_001_val_1_bismark_bt2_pe._10x.bedgraph\n", "c5b3af5e461f0e8b16dbec1147302053\tMeth11_R1_001_val_1_bismark_bt2_pe._10x.bedgraph\n", "018e0688b2ba9b648690a4f9e6852f3a\tMeth12_R1_001_val_1_bismark_bt2_pe._10x.bedgraph\n", "2824840442d6aaa25f35e6317e607bc5\tMeth16_R1_001_val_1_bismark_bt2_pe._10x.bedgraph\n", "930dea1323af4e158f349ae3496273b6\tMeth17_R1_001_val_1_bismark_bt2_pe._10x.bedgraph\n", "6732e0d5547d88767f2100ef37868fae\tMeth18_R1_001_val_1_bismark_bt2_pe._10x.bedgraph\n", "c98583d7fda3eb3e8761b2128ebd4d21\tMeth15_R1_001_val_1_bismark_bt2_pe._10x.bedgraph\n", "96cf84339426f4d54ca71786cd4038dd\tMeth14_R1_001_val_1_bismark_bt2_pe._10x.bedgraph\n", "df2821f5f7c8ab6e30580ab1d27c4aa4\tMeth13_R1_001_val_1_bismark_bt2_pe._10x.bedgraph\n", " 9 Mcap-10xbedgraph-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-10xbedgraph-GANNET-md5sum-hashes.txt Mcap-10xbedgraph-GANNET-md5sum-paths.txt \\\n", "> Mcap-10xbedgraph-GANNET-md5sum.txt\n", "!head Mcap-10xbedgraph-GANNET-md5sum.txt\n", "!wc -l Mcap-10xbedgraph-GANNET-md5sum.txt" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "### *P. acuta*" ] }, { "cell_type": "code", "execution_count": 9, "metadata": {}, "outputs": [], "source": [ "#Get all lines from original checksum document\n", "#Extract information for 10x 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 10x.bedgraph \\\n", "| grep Pact \\\n", "| cut -c1-32 \\\n", "> Pact-10xbedgraph-GANNET-md5sum-hashes.txt" ] }, { "cell_type": "code", "execution_count": 10, "metadata": {}, "outputs": [], "source": [ "#Get all lines from original checksum document\n", "#Extract information for 10x bedgraphs\n", "#Extract information for Pact data only\n", "#Reverse order of characters in each line\n", "#Only keep the first 47 characters in each line\n", "#actually the last 47 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 10x.bedgraph \\\n", "| grep Pact \\\n", "| rev \\\n", "| cut -c1-47 \\\n", "| rev \\\n", "> Pact-10xbedgraph-GANNET-md5sum-paths.txt" ] }, { "cell_type": "code", "execution_count": 11, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "6a44284135a731f293f85a935322a215\tMeth8_R1_001_val_1_bismark_bt2_pe._10x.bedgraph\n", "f45ac7a1e54fd8aae6e3cacf1a97e7db\tMeth7_R1_001_val_1_bismark_bt2_pe._10x.bedgraph\n", "e053db8611247e56d726029093c2992d\tMeth9_R1_001_val_1_bismark_bt2_pe._10x.bedgraph\n", "ceb247496486993d0a56790dfcfc4c6a\tMeth2_R1_001_val_1_bismark_bt2_pe._10x.bedgraph\n", "02f3fe5af0182a75ab0390bb02f5d327\tMeth3_R1_001_val_1_bismark_bt2_pe._10x.bedgraph\n", "960c22c08200ddaf7f5c94bd7a5a355a\tMeth1_R1_001_val_1_bismark_bt2_pe._10x.bedgraph\n", "76a658a7f56479c417714e06fc2bd29c\tMeth6_R1_001_val_1_bismark_bt2_pe._10x.bedgraph\n", "bdc7b6bbddebb741a364ec35925fe765\tMeth5_R1_001_val_1_bismark_bt2_pe._10x.bedgraph\n", "77ebb1de8a3e334a4737090be95ee1f8\tMeth4_R1_001_val_1_bismark_bt2_pe._10x.bedgraph\n", " 9 Pact-10xbedgraph-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-10xbedgraph-GANNET-md5sum-hashes.txt Pact-10xbedgraph-GANNET-md5sum-paths.txt \\\n", "> Pact-10xbedgraph-GANNET-md5sum.txt\n", "!head Pact-10xbedgraph-GANNET-md5sum.txt\n", "!wc -l Pact-10xbedgraph-GANNET-md5sum.txt" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "## *M. capitata*" ] }, { "cell_type": "code", "execution_count": 36, "metadata": { "collapsed": true }, "outputs": [], "source": [ "#Make a directory for Mcap output\n", "#!mkdir Mcap" ] }, { "cell_type": "code", "execution_count": 12, "metadata": { "scrolled": true }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "/Users/yaaminivenkataraman/Documents/Meth_Compare/analyses/Characterizing-CpG-Methylation/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": 44, "metadata": { "collapsed": true }, "outputs": [], "source": [ "bedtoolsDirectory = \"/usr/local/bin/\"" ] }, { "cell_type": "code", "execution_count": 35, "metadata": { "collapsed": true }, "outputs": [], "source": [ "mcGenes = \"../../../genome-feature-files/Mcap.GFFannotation.gene.gff\"" ] }, { "cell_type": "code", "execution_count": 36, "metadata": { "collapsed": true }, "outputs": [], "source": [ "mcCDS = \"../../../genome-feature-files/Mcap.GFFannotation.CDS.gff\"" ] }, { "cell_type": "code", "execution_count": 37, "metadata": { "collapsed": true }, "outputs": [], "source": [ "mcIntron = \"../../../genome-feature-files/Mcap.GFFannotation.intron.gff\"" ] }, { "cell_type": "code", "execution_count": 38, "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": 39, "metadata": {}, "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", " 53875 ../../../genome-feature-files/Mcap.GFFannotation.gene.gff\n" ] } ], "source": [ "!head {mcGenes}\n", "!wc -l {mcGenes}" ] }, { "cell_type": "code", "execution_count": 40, "metadata": {}, "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", " 224096 ../../../genome-feature-files/Mcap.GFFannotation.CDS.gff\n" ] } ], "source": [ "!head {mcCDS}\n", "!wc -l {mcCDS}" ] }, { "cell_type": "code", "execution_count": 41, "metadata": {}, "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", " 170950 ../../../genome-feature-files/Mcap.GFFannotation.intron.gff\n" ] } ], "source": [ "!head {mcIntron}\n", "!wc -l {mcIntron}" ] }, { "cell_type": "code", "execution_count": 42, "metadata": { "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": 21, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "\r\n", "Tool: bedtools intersect (aka intersectBed)\r\n", "Version: v2.29.2\r\n", "Summary: Report overlaps between two feature files.\r\n", "\r\n", "Usage: bedtools intersect [OPTIONS] -a -b \r\n", "\r\n", "\tNote: -b may be followed with multiple databases and/or \r\n", "\twildcard (*) character(s). \r\n", "Options: \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, -F, -r, and -s.\r\n", "\r\n", "\t-C\tFor each entry in A, separately report the number of\r\n", "\t\t- overlaps with each B file on a distinct line.\r\n", "\t\t- Reports 0 for A entries that have no overlap with B.\r\n", "\t\t- Overlaps restricted by -f, -F, -r, and -s.\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-ubam\tWrite uncompressed BAM output. Default writes compressed BAM.\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-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-F\tMinimum overlap required as a fraction of B.\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-e\tRequire that the minimum fraction be satisfied for A OR B.\r\n", "\t\t- In other words, if -e is used with -f 0.90 and -F 0.10 this requires\r\n", "\t\t that either 90% of A is covered OR 10% of B is covered.\r\n", "\t\t Without -e, both fractions would have to be satisfied.\r\n", "\r\n", "\t-split\tTreat \"split\" BAM or BED12 entries as distinct BED intervals.\r\n", "\r\n", "\t-g\tProvide a genome file to enforce consistent chromosome sort order\r\n", "\t\tacross input files. Only applies when used with -sorted option.\r\n", "\r\n", "\t-nonamecheck\tFor sorted data, don't throw an error if the file has different naming conventions\r\n", "\t\t\tfor the same chromosome. ex. \"chr1\" vs \"chr01\".\r\n", "\r\n", "\t-sorted\tUse the \"chromsweep\" algorithm for sorted (-k1,1 -k2,2n) input.\r\n", "\r\n", "\t-names\tWhen using multiple databases, provide an alias for each that\r\n", "\t\twill appear instead of a fileId when also printing the DB record.\r\n", "\r\n", "\t-filenames\tWhen using multiple databases, show each complete filename\r\n", "\t\t\tinstead of a fileId when also printing the DB record.\r\n", "\r\n", "\t-sortout\tWhen using multiple databases, sort the output DB hits\r\n", "\t\t\tfor each record.\r\n", "\r\n", "\t-bed\tIf using BAM input, write output as BED.\r\n", "\r\n", "\t-header\tPrint the header from the A file prior to results.\r\n", "\r\n", "\t-nobuf\tDisable buffered output. Using this option will cause each line\r\n", "\t\tof output to be printed as it is generated, rather than saved\r\n", "\t\tin a buffer. This will make printing large output files \r\n", "\t\tnoticeably slower, but can be useful in conjunction with\r\n", "\t\tother software tools and scripts that need to process one\r\n", "\t\tline of bedtools output at a time.\r\n", "\r\n", "\t-iobuf\tSpecify amount of memory to use for input buffer.\r\n", "\t\tTakes an integer argument. Optional suffixes K/M/G supported.\r\n", "\t\tNote: currently has no effect with compressed files.\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 excluded 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", "\r\n", "\r\n", "\r\n" ] } ], "source": [ "!{bedtoolsDirectory}intersectBed -h" ] }, { "cell_type": "code", "execution_count": 45, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ " 9450564\n", "CG motif overlaps with genes\n" ] } ], "source": [ "!{bedtoolsDirectory}intersectBed \\\n", "-u \\\n", "-a {mcCGMotifs} \\\n", "-b {mcGenes} \\\n", "| wc -l\n", "!echo \"CG motif overlaps with genes\"" ] }, { "cell_type": "code", "execution_count": 46, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ " 1953206\n", "CG motif overlaps with coding sequences (CDS)\n" ] } ], "source": [ "!{bedtoolsDirectory}intersectBed \\\n", "-u \\\n", "-a {mcCGMotifs} \\\n", "-b {mcCDS} \\\n", "| wc -l\n", "!echo \"CG motif overlaps with coding sequences (CDS)\"" ] }, { "cell_type": "code", "execution_count": 47, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ " 7503314\n", "CG motif overlaps with introns\n" ] } ], "source": [ "!{bedtoolsDirectory}intersectBed \\\n", "-u \\\n", "-a {mcCGMotifs} \\\n", "-b {mcIntron} \\\n", "| wc -l\n", "!echo \"CG motif overlaps with introns\"" ] }, { "cell_type": "code", "execution_count": 48, "metadata": { "scrolled": true }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ " 19224826\n", "CG motif overlaps that do not overlap with genes (i.e. intergenic regions)\n" ] } ], "source": [ "!{bedtoolsDirectory}intersectBed \\\n", "-v \\\n", "-a {mcCGMotifs} \\\n", "-b {mcGenes} \\\n", "| wc -l\n", "!echo \"CG motif overlaps that do not overlap with genes (i.e. intergenic regions)\"" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "#### 1d. Summary" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "| *M. capitata* Genome Feature \t| Number individual features \t| **Overlaps with CG Motifs** \t| **% Total CG Motifs** \t|\n", "|:----------------------------------:\t|:------------------------------:\t|:---------------------------:\t|:--------------------:\t|\n", "| Genes \t| 458273 \t| 9450564 \t| 32.9 \t|\n", "| Coding Sequences \t| 283926 \t| 1953206 \t| 6.8 \t|\n", "| Introns \t| 221428 \t| 7503314 \t| 26.2 \t|\n", "| Intergenic Regions \t| N/A \t| 19224826 \t| 67.0 \t|" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "### 2. Download coverage files" ] }, { "cell_type": "code", "execution_count": 5, "metadata": { "scrolled": true }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "--2020-04-13 10:36:29-- https://gannet.fish.washington.edu/seashell/bu-mox/scrubbed/031520-TG-bs/Mcap_tg/dedup/\n", "Resolving gannet.fish.washington.edu... 128.95.149.52\n", "Connecting to 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 0.09s \n", "\n", "2020-04-13 10:36:31 (470 KB/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", "--2020-04-13 10:36:31-- 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", "2020-04-13 10:36:31 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", "--2020-04-13 10:36:31-- 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 0.09s \n", "\n", "2020-04-13 10:36:32 (478 KB/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", "--2020-04-13 10:36:32-- 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 0.09s \n", "\n", "2020-04-13 10:36:33 (446 KB/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", "--2020-04-13 10:36:33-- 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 0.09s \n", "\n", "2020-04-13 10:36:34 (476 KB/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", "--2020-04-13 10:36:34-- 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 0.09s \n", "\n", "2020-04-13 10:36:35 (471 KB/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", "--2020-04-13 10:36:35-- https://gannet.fish.washington.edu/seashell/bu-mox/scrubbed/031520-TG-bs/Mcap_tg/dedup/Meth10_R1_001_val_1_bismark_bt2_pe._10x.bedgraph\n", "Reusing existing connection to gannet.fish.washington.edu:443.\n", "HTTP request sent, awaiting response... 200 OK\n", "Length: 12666429 (12M)\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._10x.bedgraph’\n", "\n", "gannet.fish.washing 100%[===================>] 12.08M 2.64MB/s in 5.4s \n", "\n", "2020-04-13 10:36:41 (2.25 MB/s) - ‘gannet.fish.washington.edu/seashell/bu-mox/scrubbed/031520-TG-bs/Mcap_tg/dedup/Meth10_R1_001_val_1_bismark_bt2_pe._10x.bedgraph’ saved [12666429/12666429]\n", "\n", "--2020-04-13 10:36:41-- https://gannet.fish.washington.edu/seashell/bu-mox/scrubbed/031520-TG-bs/Mcap_tg/dedup/Meth11_R1_001_val_1_bismark_bt2_pe._10x.bedgraph\n", "Reusing existing connection to gannet.fish.washington.edu:443.\n", "HTTP request sent, awaiting response... 200 OK\n", "Length: 12910664 (12M)\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._10x.bedgraph’\n", "\n", "gannet.fish.washing 100%[===================>] 12.31M 1.90MB/s in 6.5s \n", "\n", "2020-04-13 10:36:47 (1.88 MB/s) - ‘gannet.fish.washington.edu/seashell/bu-mox/scrubbed/031520-TG-bs/Mcap_tg/dedup/Meth11_R1_001_val_1_bismark_bt2_pe._10x.bedgraph’ saved [12910664/12910664]\n", "\n", "--2020-04-13 10:36:47-- https://gannet.fish.washington.edu/seashell/bu-mox/scrubbed/031520-TG-bs/Mcap_tg/dedup/Meth12_R1_001_val_1_bismark_bt2_pe._10x.bedgraph\n", "Reusing existing connection to gannet.fish.washington.edu:443.\n", "HTTP request sent, awaiting response... 200 OK\n", "Length: 47288456 (45M)\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._10x.bedgraph’\n", "\n", "gannet.fish.washing 100%[===================>] 45.10M 2.65MB/s in 22s \n", "\n", "2020-04-13 10:37:10 (2.03 MB/s) - ‘gannet.fish.washington.edu/seashell/bu-mox/scrubbed/031520-TG-bs/Mcap_tg/dedup/Meth12_R1_001_val_1_bismark_bt2_pe._10x.bedgraph’ saved [47288456/47288456]\n", "\n", "--2020-04-13 10:37:10-- https://gannet.fish.washington.edu/seashell/bu-mox/scrubbed/031520-TG-bs/Mcap_tg/dedup/Meth16_R1_001_val_1_bismark_bt2_pe._10x.bedgraph\n", "Reusing existing connection to gannet.fish.washington.edu:443.\n", "HTTP request sent, awaiting response... 200 OK\n", "Length: 1196669 (1.1M)\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._10x.bedgraph’\n", "\n", "gannet.fish.washing 100%[===================>] 1.14M 2.52MB/s in 0.5s \n", "\n", "2020-04-13 10:37:10 (2.52 MB/s) - ‘gannet.fish.washington.edu/seashell/bu-mox/scrubbed/031520-TG-bs/Mcap_tg/dedup/Meth16_R1_001_val_1_bismark_bt2_pe._10x.bedgraph’ saved [1196669/1196669]\n", "\n", "--2020-04-13 10:37:10-- https://gannet.fish.washington.edu/seashell/bu-mox/scrubbed/031520-TG-bs/Mcap_tg/dedup/Meth17_R1_001_val_1_bismark_bt2_pe._10x.bedgraph\n", "Reusing existing connection to gannet.fish.washington.edu:443.\n", "HTTP request sent, awaiting response... 200 OK\n", "Length: 588466 (575K)\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._10x.bedgraph’\n", "\n", "gannet.fish.washing 100%[===================>] 574.67K 2.27MB/s in 0.2s \n", "\n", "2020-04-13 10:37:11 (2.27 MB/s) - ‘gannet.fish.washington.edu/seashell/bu-mox/scrubbed/031520-TG-bs/Mcap_tg/dedup/Meth17_R1_001_val_1_bismark_bt2_pe._10x.bedgraph’ saved [588466/588466]\n", "\n", "--2020-04-13 10:37:11-- https://gannet.fish.washington.edu/seashell/bu-mox/scrubbed/031520-TG-bs/Mcap_tg/dedup/Meth18_R1_001_val_1_bismark_bt2_pe._10x.bedgraph\n", "Reusing existing connection to gannet.fish.washington.edu:443.\n", "HTTP request sent, awaiting response... 200 OK\n", "Length: 400635 (391K)\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._10x.bedgraph’\n", "\n", "gannet.fish.washing 100%[===================>] 391.25K 1.73MB/s in 0.2s \n", "\n", "2020-04-13 10:37:11 (1.73 MB/s) - ‘gannet.fish.washington.edu/seashell/bu-mox/scrubbed/031520-TG-bs/Mcap_tg/dedup/Meth18_R1_001_val_1_bismark_bt2_pe._10x.bedgraph’ saved [400635/400635]\n", "\n", "FINISHED --2020-04-13 10:37:11--\n", "Total wall clock time: 42s\n", "Downloaded: 11 files, 72M in 36s (2.02 MB/s)\n" ] } ], "source": [ "#Download Mcap WGBS and MBD-BS 10x sample bedgraphs\n", "!wget -r -l1 --no-parent -A \"*10x.bedgraph\" https://gannet.fish.washington.edu/seashell/bu-mox/scrubbed/031520-TG-bs/Mcap_tg/dedup/" ] }, { "cell_type": "code", "execution_count": 7, "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": 8, "metadata": { "collapsed": true }, "outputs": [], "source": [ "#Remove empty directory\n", "!rm -r gannet.fish.washington.edu/" ] }, { "cell_type": "code", "execution_count": 11, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "Meth10_R1_001_val_1_bismark_bt2_pe._10x.bedgraph\r\n", "Meth11_R1_001_val_1_bismark_bt2_pe._10x.bedgraph\r\n", "Meth12_R1_001_val_1_bismark_bt2_pe._10x.bedgraph\r\n", "Meth16_R1_001_val_1_bismark_bt2_pe._10x.bedgraph\r\n", "Meth17_R1_001_val_1_bismark_bt2_pe._10x.bedgraph\r\n", "Meth18_R1_001_val_1_bismark_bt2_pe._10x.bedgraph\r\n" ] } ], "source": [ "#Check downloaded files\n", "!ls *bedgraph" ] }, { "cell_type": "code", "execution_count": 12, "metadata": { "scrolled": true }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "--2020-04-13 10:39:10-- https://gannet.fish.washington.edu/seashell/bu-mox/scrubbed/031520-TG-bs/Mcap_tg/nodedup/\n", "Resolving gannet.fish.washington.edu... 128.95.149.52\n", "Connecting to 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 0.04s \n", "\n", "2020-04-13 10:39:11 (470 KB/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", "--2020-04-13 10:39:11-- 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", "2020-04-13 10:39:11 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", "--2020-04-13 10:39:11-- 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 0.05s \n", "\n", "2020-04-13 10:39:11 (410 KB/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", "--2020-04-13 10:39:11-- 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", "2020-04-13 10:39:11 (44.5 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", "--2020-04-13 10:39:11-- 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 0.04s \n", "\n", "2020-04-13 10:39:12 (440 KB/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", "--2020-04-13 10:39:12-- 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 0.04s \n", "\n", "2020-04-13 10:39:13 (466 KB/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", "--2020-04-13 10:39:13-- https://gannet.fish.washington.edu/seashell/bu-mox/scrubbed/031520-TG-bs/Mcap_tg/nodedup/Meth13_R1_001_val_1_bismark_bt2_pe._10x.bedgraph\n", "Reusing existing connection to gannet.fish.washington.edu:443.\n", "HTTP request sent, awaiting response... 200 OK\n", "Length: 78803082 (75M)\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._10x.bedgraph’\n", "\n", "gannet.fish.washing 100%[===================>] 75.15M 2.01MB/s in 63s \n", "\n", "2020-04-13 10:40:16 (1.20 MB/s) - ‘gannet.fish.washington.edu/seashell/bu-mox/scrubbed/031520-TG-bs/Mcap_tg/nodedup/Meth13_R1_001_val_1_bismark_bt2_pe._10x.bedgraph’ saved [78803082/78803082]\n", "\n", "--2020-04-13 10:40:16-- https://gannet.fish.washington.edu/seashell/bu-mox/scrubbed/031520-TG-bs/Mcap_tg/nodedup/Meth14_R1_001_val_1_bismark_bt2_pe._10x.bedgraph\n", "Reusing existing connection to gannet.fish.washington.edu:443.\n", "HTTP request sent, awaiting response... 200 OK\n", "Length: 61800474 (59M)\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._10x.bedgraph’\n", "\n", "gannet.fish.washing 100%[===================>] 58.94M 1.71MB/s in 33s \n", "\n", "2020-04-13 10:40:49 (1.79 MB/s) - ‘gannet.fish.washington.edu/seashell/bu-mox/scrubbed/031520-TG-bs/Mcap_tg/nodedup/Meth14_R1_001_val_1_bismark_bt2_pe._10x.bedgraph’ saved [61800474/61800474]\n", "\n", "--2020-04-13 10:40:49-- https://gannet.fish.washington.edu/seashell/bu-mox/scrubbed/031520-TG-bs/Mcap_tg/nodedup/Meth15_R1_001_val_1_bismark_bt2_pe._10x.bedgraph\n", "Reusing existing connection to gannet.fish.washington.edu:443.\n", "HTTP request sent, awaiting response... 200 OK\n", "Length: 76890794 (73M)\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._10x.bedgraph’\n", "\n", "gannet.fish.washing 100%[===================>] 73.33M 2.35MB/s in 32s \n", "\n", "2020-04-13 10:41:21 (2.30 MB/s) - ‘gannet.fish.washington.edu/seashell/bu-mox/scrubbed/031520-TG-bs/Mcap_tg/nodedup/Meth15_R1_001_val_1_bismark_bt2_pe._10x.bedgraph’ saved [76890794/76890794]\n", "\n", "FINISHED --2020-04-13 10:41:21--\n", "Total wall clock time: 2m 11s\n", "Downloaded: 8 files, 208M in 2m 8s (1.62 MB/s)\n" ] } ], "source": [ "#Download Mcap RRBS 10x sample bedgraphs\n", "!wget -r -l1 --no-parent -A \"*10x.bedgraph\" https://gannet.fish.washington.edu/seashell/bu-mox/scrubbed/031520-TG-bs/Mcap_tg/nodedup/" ] }, { "cell_type": "code", "execution_count": 13, "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": 14, "metadata": { "collapsed": true }, "outputs": [], "source": [ "#Remove empty directory\n", "!rm -r gannet.fish.washington.edu/" ] }, { "cell_type": "code", "execution_count": 15, "metadata": { "scrolled": true }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "Meth10_R1_001_val_1_bismark_bt2_pe._10x.bedgraph\r\n", "Meth11_R1_001_val_1_bismark_bt2_pe._10x.bedgraph\r\n", "Meth12_R1_001_val_1_bismark_bt2_pe._10x.bedgraph\r\n", "Meth13_R1_001_val_1_bismark_bt2_pe._10x.bedgraph\r\n", "Meth14_R1_001_val_1_bismark_bt2_pe._10x.bedgraph\r\n", "Meth15_R1_001_val_1_bismark_bt2_pe._10x.bedgraph\r\n", "Meth16_R1_001_val_1_bismark_bt2_pe._10x.bedgraph\r\n", "Meth17_R1_001_val_1_bismark_bt2_pe._10x.bedgraph\r\n", "Meth18_R1_001_val_1_bismark_bt2_pe._10x.bedgraph\r\n" ] } ], "source": [ "!find *bedgraph" ] }, { "cell_type": "code", "execution_count": null, "metadata": {}, "outputs": [], "source": [ "#Verify checksums from gannet\n", "!md5sum -c ../Mcap-10xbedgraph-GANNET-md5sum.txt" ] }, { "cell_type": "code", "execution_count": 16, "metadata": { "scrolled": true }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ " 470893 Meth10_R1_001_val_1_bismark_bt2_pe._10x.bedgraph\n", " 479520 Meth11_R1_001_val_1_bismark_bt2_pe._10x.bedgraph\n", " 1756997 Meth12_R1_001_val_1_bismark_bt2_pe._10x.bedgraph\n", " 2945967 Meth13_R1_001_val_1_bismark_bt2_pe._10x.bedgraph\n", " 2310457 Meth14_R1_001_val_1_bismark_bt2_pe._10x.bedgraph\n", " 2874355 Meth15_R1_001_val_1_bismark_bt2_pe._10x.bedgraph\n", " 44091 Meth16_R1_001_val_1_bismark_bt2_pe._10x.bedgraph\n", " 21797 Meth17_R1_001_val_1_bismark_bt2_pe._10x.bedgraph\n", " 14818 Meth18_R1_001_val_1_bismark_bt2_pe._10x.bedgraph\n", " 10918895 total\n" ] } ], "source": [ "!wc -l *bedgraph" ] }, { "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": 17, "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": 18, "metadata": { "scrolled": true }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "==> Meth10_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-Meth <==\r\n", "1 448144 448146 76.923077\r\n", "1 789544 789546 50.000000\r\n", "1 789590 789592 50.000000\r\n", "1 876587 876589 100.000000\r\n", "1 876606 876608 63.636364\r\n", "1 1267992 1267994 100.000000\r\n", "1 1269495 1269497 100.000000\r\n", "1 1269508 1269510 83.333333\r\n", "1 1269532 1269534 100.000000\r\n", "1 1373604 1373606 78.571429\r\n", "\r\n", "==> Meth11_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-Meth <==\r\n", "1 448144 448146 63.636364\r\n", "1 450663 450665 83.333333\r\n", "1 450675 450677 81.818182\r\n", "1 450703 450705 80.000000\r\n", "1 744619 744621 54.545455\r\n", "1 1264052 1264054 100.000000\r\n", "1 1269495 1269497 90.000000\r\n", "1 1269508 1269510 80.000000\r\n", "1 1269532 1269534 100.000000\r\n", "1 1273421 1273423 90.909091\r\n", "\r\n", "==> Meth12_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-Meth <==\r\n", "1 69151 69153 90.909091\r\n", "1 69235 69237 80.000000\r\n", "1 69580 69582 100.000000\r\n", "1 69584 69586 100.000000\r\n", "1 69845 69847 100.000000\r\n", "1 69882 69884 100.000000\r\n", "1 70019 70021 91.666667\r\n", "1 70068 70070 100.000000\r\n", "1 70083 70085 100.000000\r\n", "1 70129 70131 100.000000\r\n", "\r\n", "==> Meth13_R1_001_val_1_bismark_bt2_pe._10x.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 80721 80723 58.000000\r\n", "1 101462 101464 100.000000\r\n", "1 101535 101537 96.666667\r\n", "1 108331 108333 100.000000\r\n", "1 108383 108385 100.000000\r\n", "1 108427 108429 100.000000\r\n", "\r\n", "==> Meth14_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-Meth <==\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 317029 317031 100.000000\r\n", "1 336217 336219 68.367347\r\n", "1 455318 455320 60.000000\r\n", "1 527701 527703 100.000000\r\n", "1 616272 616274 57.142857\r\n", "1 759941 759943 64.285714\r\n", "\r\n", "==> Meth15_R1_001_val_1_bismark_bt2_pe._10x.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._10x.bedgraph-Meth <==\r\n", "1 1536523 1536525 81.818182\r\n", "1 1536643 1536645 70.000000\r\n", "1 1536657 1536659 72.727273\r\n", "1 1755684 1755686 90.000000\r\n", "1 1958635 1958637 100.000000\r\n", "1 1958667 1958669 90.000000\r\n", "1 1958693 1958695 100.000000\r\n", "1 1958702 1958704 90.000000\r\n", "1 2069354 2069356 80.000000\r\n", "1 2069356 2069358 80.000000\r\n", "\r\n", "==> Meth17_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-Meth <==\r\n", "1 1987244 1987246 100.000000\r\n", "1 1987263 1987265 100.000000\r\n", "2 2679583 2679585 80.000000\r\n", "2 2679593 2679595 80.000000\r\n", "2 2680034 2680036 50.000000\r\n", "2 2881267 2881269 90.909091\r\n", "2 2902772 2902774 100.000000\r\n", "2 3037511 3037513 90.000000\r\n", "2 3037528 3037530 90.000000\r\n", "2 3225309 3225311 83.333333\r\n", "\r\n", "==> Meth18_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-Meth <==\r\n", "1 3129772 3129774 100.000000\r\n", "1 3129793 3129795 100.000000\r\n", "1 3129805 3129807 100.000000\r\n", "2 330308 330310 100.000000\r\n", "2 330327 330329 90.909091\r\n", "2 330330 330332 100.000000\r\n", "2 330347 330349 92.307692\r\n", "2 330364 330366 91.666667\r\n", "2 330370 330372 100.000000\r\n", "2 330517 330519 100.000000\r\n" ] } ], "source": [ "!head *Meth" ] }, { "cell_type": "code", "execution_count": 19, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ " 35488 Meth10_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-Meth\r\n", " 49640 Meth11_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-Meth\r\n", " 173085 Meth12_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-Meth\r\n", " 204797 Meth13_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-Meth\r\n", " 136505 Meth14_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-Meth\r\n", " 172957 Meth15_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-Meth\r\n", " 16168 Meth16_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-Meth\r\n", " 6080 Meth17_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-Meth\r\n", " 4837 Meth18_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-Meth\r\n", " 799557 total\r\n" ] } ], "source": [ "!wc -l *Meth" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "##### Sparsely methylated loci" ] }, { "cell_type": "code", "execution_count": 20, "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": 21, "metadata": { "scrolled": true }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "==> Meth10_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-sparseMeth <==\r\n", "1 405936 405938 18.181818\r\n", "1 437346 437348 18.181818\r\n", "1 437349 437351 18.181818\r\n", "1 460307 460309 15.384615\r\n", "1 463857 463859 18.181818\r\n", "1 527701 527703 15.384615\r\n", "1 527706 527708 15.384615\r\n", "1 527726 527728 15.384615\r\n", "1 527739 527741 13.333333\r\n", "1 601991 601993 20.000000\r\n", "\r\n", "==> Meth11_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-sparseMeth <==\r\n", "1 219905 219907 15.384615\r\n", "1 230777 230779 18.181818\r\n", "1 272290 272292 20.000000\r\n", "1 411793 411795 20.000000\r\n", "1 425364 425366 16.666667\r\n", "1 460884 460886 18.181818\r\n", "1 460920 460922 23.529412\r\n", "1 460947 460949 20.000000\r\n", "1 460953 460955 13.333333\r\n", "1 461445 461447 16.666667\r\n", "\r\n", "==> Meth12_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-sparseMeth <==\r\n", "1 79955 79957 16.666667\r\n", "1 205989 205991 15.789474\r\n", "1 216074 216076 15.384615\r\n", "1 243227 243229 18.181818\r\n", "1 273081 273083 25.000000\r\n", "1 356393 356395 20.000000\r\n", "1 380405 380407 28.571429\r\n", "1 380486 380488 25.000000\r\n", "1 382279 382281 16.666667\r\n", "1 382287 382289 18.750000\r\n", "\r\n", "==> Meth13_R1_001_val_1_bismark_bt2_pe._10x.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 169847 169849 12.820513\r\n", "1 198078 198080 30.434783\r\n", "1 227400 227402 18.750000\r\n", "1 227407 227409 17.187500\r\n", "1 227416 227418 13.953488\r\n", "\r\n", "==> Meth14_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-sparseMeth <==\r\n", "1 166013 166015 12.500000\r\n", "1 227400 227402 11.200000\r\n", "1 246955 246957 29.545455\r\n", "1 248898 248900 13.333333\r\n", "1 305489 305491 11.111111\r\n", "1 309954 309956 10.526316\r\n", "1 314160 314162 32.352941\r\n", "1 314207 314209 16.666667\r\n", "1 314212 314214 20.833333\r\n", "1 320382 320384 11.111111\r\n", "\r\n", "==> Meth15_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-sparseMeth <==\r\n", "1 41916 41918 13.043478\r\n", "1 42261 42263 16.666667\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", "1 170097 170099 22.857143\r\n", "\r\n", "==> Meth16_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-sparseMeth <==\r\n", "1 1540374 1540376 30.000000\r\n", "2 330579 330581 31.250000\r\n", "2 1463459 1463461 36.363636\r\n", "2 1463493 1463495 36.363636\r\n", "2 1463513 1463515 33.333333\r\n", "2 1463518 1463520 25.000000\r\n", "2 1463525 1463527 33.333333\r\n", "2 1463591 1463593 16.666667\r\n", "2 1704675 1704677 27.272727\r\n", "2 1704686 1704688 30.769231\r\n", "\r\n", "==> Meth17_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-sparseMeth <==\r\n", "2 1753367 1753369 30.000000\r\n", "2 2676061 2676063 18.181818\r\n", "2 2680138 2680140 15.000000\r\n", "2 2680144 2680146 23.529412\r\n", "2 2750686 2750688 36.363636\r\n", "2 2750688 2750690 36.363636\r\n", "2 3225324 3225326 20.000000\r\n", "2 3234908 3234910 27.272727\r\n", "4 811595 811597 13.333333\r\n", "4 811607 811609 20.000000\r\n", "\r\n", "==> Meth18_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-sparseMeth <==\r\n", "1 3250296 3250298 23.076923\r\n", "4 2280510 2280512 12.162162\r\n", "4 2282559 2282561 15.000000\r\n", "4 2282561 2282563 17.391304\r\n", "4 2761930 2761932 16.666667\r\n", "4 2761958 2761960 12.765957\r\n", "5 1381856 1381858 11.764706\r\n", "6 2158174 2158176 40.000000\r\n", "7 86796 86798 45.454545\r\n", "7 1092583 1092585 14.285714\r\n" ] } ], "source": [ "!head *sparseMeth" ] }, { "cell_type": "code", "execution_count": 22, "metadata": { "scrolled": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ " 43405 Meth10_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-sparseMeth\r\n", " 42459 Meth11_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-sparseMeth\r\n", " 127160 Meth12_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-sparseMeth\r\n", " 129206 Meth13_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-sparseMeth\r\n", " 107375 Meth14_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-sparseMeth\r\n", " 145976 Meth15_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-sparseMeth\r\n", " 5283 Meth16_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-sparseMeth\r\n", " 2282 Meth17_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-sparseMeth\r\n", " 1433 Meth18_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-sparseMeth\r\n", " 604579 total\r\n" ] } ], "source": [ "!wc -l *sparseMeth" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "##### Unmethylated loci" ] }, { "cell_type": "code", "execution_count": 23, "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": 24, "metadata": { "scrolled": true }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "==> Meth10_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-unMeth <==\r\n", "1 208521 208523 0.000000\r\n", "1 208524 208526 0.000000\r\n", "1 212911 212913 0.000000\r\n", "1 213160 213162 0.000000\r\n", "1 213207 213209 0.000000\r\n", "1 213247 213249 0.000000\r\n", "1 213252 213254 0.000000\r\n", "1 217269 217271 0.000000\r\n", "1 217349 217351 10.000000\r\n", "1 238052 238054 0.000000\r\n", "\r\n", "==> Meth11_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-unMeth <==\r\n", "1 6453 6455 0.000000\r\n", "1 6484 6486 0.000000\r\n", "1 221750 221752 10.000000\r\n", "1 223373 223375 0.000000\r\n", "1 229852 229854 0.000000\r\n", "1 230363 230365 0.000000\r\n", "1 230742 230744 0.000000\r\n", "1 230854 230856 0.000000\r\n", "1 232150 232152 0.000000\r\n", "1 233751 233753 0.000000\r\n", "\r\n", "==> Meth12_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-unMeth <==\r\n", "1 5243 5245 10.000000\r\n", "1 5296 5298 0.000000\r\n", "1 5332 5334 0.000000\r\n", "1 5343 5345 0.000000\r\n", "1 5368 5370 8.333333\r\n", "1 5665 5667 0.000000\r\n", "1 5737 5739 0.000000\r\n", "1 5749 5751 0.000000\r\n", "1 5751 5753 0.000000\r\n", "1 6320 6322 0.000000\r\n", "\r\n", "==> Meth13_R1_001_val_1_bismark_bt2_pe._10x.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._10x.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 12314 12316 0.000000\r\n", "1 12331 12333 0.000000\r\n", "1 12350 12352 0.000000\r\n", "1 12352 12354 0.000000\r\n", "1 12364 12366 0.000000\r\n", "1 12383 12385 0.000000\r\n", "\r\n", "==> Meth15_R1_001_val_1_bismark_bt2_pe._10x.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._10x.bedgraph-unMeth <==\r\n", "1 2111902 2111904 10.000000\r\n", "1 2111995 2111997 0.000000\r\n", "1 2112003 2112005 0.000000\r\n", "1 2112031 2112033 0.000000\r\n", "1 2112033 2112035 10.000000\r\n", "1 2112044 2112046 0.000000\r\n", "1 2311899 2311901 0.000000\r\n", "1 2311908 2311910 0.000000\r\n", "1 2420948 2420950 0.000000\r\n", "1 2420953 2420955 0.000000\r\n", "\r\n", "==> Meth17_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-unMeth <==\r\n", "1 832598 832600 0.000000\r\n", "1 2528819 2528821 0.000000\r\n", "1 2528872 2528874 0.000000\r\n", "1 2528900 2528902 0.000000\r\n", "1 2529124 2529126 0.000000\r\n", "1 2608371 2608373 0.000000\r\n", "1 3052318 3052320 0.000000\r\n", "1 3052336 3052338 0.000000\r\n", "2 1780979 1780981 0.000000\r\n", "2 1781016 1781018 0.000000\r\n", "\r\n", "==> Meth18_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-unMeth <==\r\n", "1 1620404 1620406 0.000000\r\n", "1 2528872 2528874 0.000000\r\n", "1 2528900 2528902 6.666667\r\n", "1 2529124 2529126 5.555556\r\n", "1 3161844 3161846 6.666667\r\n", "1 3161850 3161852 6.666667\r\n", "1 3161856 3161858 6.666667\r\n", "1 3161865 3161867 0.000000\r\n", "1 3161905 3161907 0.000000\r\n", "1 3248218 3248220 0.000000\r\n" ] } ], "source": [ "!head *unMeth" ] }, { "cell_type": "code", "execution_count": 25, "metadata": { "scrolled": true }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ " 392000 Meth10_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-unMeth\n", " 387421 Meth11_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-unMeth\n", " 1456752 Meth12_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-unMeth\n", " 2611964 Meth13_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-unMeth\n", " 2066577 Meth14_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-unMeth\n", " 2555422 Meth15_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-unMeth\n", " 22640 Meth16_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-unMeth\n", " 13435 Meth17_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-unMeth\n", " 8548 Meth18_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-unMeth\n", " 9514759 total\n" ] } ], "source": [ "!wc -l *unMeth" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "##### Summary" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "| **Sample** \t| **Method** \t| **CpG with Data** \t| **Methylated CpG** \t| **Sparsely Methylated CpG** \t| **Unmethylated CpG** \t|\n", "|:----------:\t|:----------:\t|:-----------------:\t|:------------------:\t|:---------------------------:\t|:--------------------:\t|\n", "| 10 \t| WGBS \t| 470893 \t| 35488 (7.5%) \t| 43405 (9.2%) \t| 392000 (83.2%) \t|\n", "| 11 \t| WGBS \t| 479520 \t| 49640 (10.3%) \t| 42459 (8.9%) \t| 387421 (80.8%) \t|\n", "| 12 \t| WGBS \t| 1756997 \t| 173085 (9.9%) \t| 127160 (7.2%) \t| 1456752 (82.9%) \t|\n", "| 13 \t| RRBS \t| 2945967 \t| 204797 (7.0%) \t| 129206 (4.4%) \t| 2611964 (88.7%) \t|\n", "| 14 \t| RRBS \t| 2310457 \t| 136505 (5.9%) \t| 107375 (4.6%) \t| 2066577 (89.4%) \t|\n", "| 15 \t| RRBS \t| 2874355 \t| 172957 (6.0%) \t| 145976 (5.1%) \t| 2555422 (88.9%) \t|\n", "| 16 \t| MBD-BSSeq \t| 44091 \t| 16168 (36.7%) \t| 5283 (12.0%) \t| 22640 (51.3%) \t|\n", "| 17 \t| MBD-BSSeq \t| 21797 \t| 6080 (27.9%) \t| 2282 (10.5%) \t| 13435 (61.6%) \t|\n", "| 18 \t| MBD-BSSeq \t| 14818 \t| 4837 (32.6%) \t| 1433 (9.7%) \t| 8548 (57.7%) \t|" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "### 4. Characterize genomic locations of CpGs" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "#### 4a. Create BEDfiles" ] }, { "cell_type": "code", "execution_count": 27, "metadata": { "scrolled": true }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ " 470893 Meth10_R1_001_val_1_bismark_bt2_pe._10x.bedgraph.bed\n", " 35488 Meth10_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-Meth.bed\n", " 43405 Meth10_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-sparseMeth.bed\n", " 392000 Meth10_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-unMeth.bed\n", " 479520 Meth11_R1_001_val_1_bismark_bt2_pe._10x.bedgraph.bed\n", " 49640 Meth11_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-Meth.bed\n", " 42459 Meth11_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-sparseMeth.bed\n", " 387421 Meth11_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-unMeth.bed\n", " 1756997 Meth12_R1_001_val_1_bismark_bt2_pe._10x.bedgraph.bed\n", " 173085 Meth12_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-Meth.bed\n", " 127160 Meth12_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-sparseMeth.bed\n", " 1456752 Meth12_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-unMeth.bed\n", " 2945967 Meth13_R1_001_val_1_bismark_bt2_pe._10x.bedgraph.bed\n", " 204797 Meth13_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-Meth.bed\n", " 129206 Meth13_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-sparseMeth.bed\n", " 2611964 Meth13_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-unMeth.bed\n", " 2310457 Meth14_R1_001_val_1_bismark_bt2_pe._10x.bedgraph.bed\n", " 136505 Meth14_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-Meth.bed\n", " 107375 Meth14_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-sparseMeth.bed\n", " 2066577 Meth14_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-unMeth.bed\n", " 2874355 Meth15_R1_001_val_1_bismark_bt2_pe._10x.bedgraph.bed\n", " 172957 Meth15_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-Meth.bed\n", " 145976 Meth15_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-sparseMeth.bed\n", " 2555422 Meth15_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-unMeth.bed\n", " 44091 Meth16_R1_001_val_1_bismark_bt2_pe._10x.bedgraph.bed\n", " 16168 Meth16_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-Meth.bed\n", " 5283 Meth16_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-sparseMeth.bed\n", " 22640 Meth16_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-unMeth.bed\n", " 21797 Meth17_R1_001_val_1_bismark_bt2_pe._10x.bedgraph.bed\n", " 6080 Meth17_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-Meth.bed\n", " 2282 Meth17_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-sparseMeth.bed\n", " 13435 Meth17_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-unMeth.bed\n", " 14818 Meth18_R1_001_val_1_bismark_bt2_pe._10x.bedgraph.bed\n", " 4837 Meth18_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-Meth.bed\n", " 1433 Meth18_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-sparseMeth.bed\n", " 8548 Meth18_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-unMeth.bed\n" ] } ], "source": [ "%%bash\n", "\n", "for f in *bedgraph*\n", "do\n", " awk '{print $1\"\\t\"$2\"\\t\"$3}' ${f} > ${f}.bed\n", " wc -l ${f}.bed\n", "done" ] }, { "cell_type": "code", "execution_count": 28, "metadata": { "scrolled": true }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "Meth10_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-Meth.bed\r\n", "Meth10_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-sparseMeth.bed\r\n", "Meth10_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-unMeth.bed\r\n", "Meth10_R1_001_val_1_bismark_bt2_pe._10x.bedgraph.bed\r\n", "Meth11_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-Meth.bed\r\n", "Meth11_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-sparseMeth.bed\r\n", "Meth11_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-unMeth.bed\r\n", "Meth11_R1_001_val_1_bismark_bt2_pe._10x.bedgraph.bed\r\n", "Meth12_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-Meth.bed\r\n", "Meth12_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-sparseMeth.bed\r\n", "Meth12_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-unMeth.bed\r\n", "Meth12_R1_001_val_1_bismark_bt2_pe._10x.bedgraph.bed\r\n", "Meth13_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-Meth.bed\r\n", "Meth13_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-sparseMeth.bed\r\n", "Meth13_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-unMeth.bed\r\n", "Meth13_R1_001_val_1_bismark_bt2_pe._10x.bedgraph.bed\r\n", "Meth14_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-Meth.bed\r\n", "Meth14_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-sparseMeth.bed\r\n", "Meth14_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-unMeth.bed\r\n", "Meth14_R1_001_val_1_bismark_bt2_pe._10x.bedgraph.bed\r\n", "Meth15_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-Meth.bed\r\n", "Meth15_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-sparseMeth.bed\r\n", "Meth15_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-unMeth.bed\r\n", "Meth15_R1_001_val_1_bismark_bt2_pe._10x.bedgraph.bed\r\n", "Meth16_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-Meth.bed\r\n", "Meth16_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-sparseMeth.bed\r\n", "Meth16_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-unMeth.bed\r\n", "Meth16_R1_001_val_1_bismark_bt2_pe._10x.bedgraph.bed\r\n", "Meth17_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-Meth.bed\r\n", "Meth17_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-sparseMeth.bed\r\n", "Meth17_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-unMeth.bed\r\n", "Meth17_R1_001_val_1_bismark_bt2_pe._10x.bedgraph.bed\r\n", "Meth18_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-Meth.bed\r\n", "Meth18_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-sparseMeth.bed\r\n", "Meth18_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-unMeth.bed\r\n", "Meth18_R1_001_val_1_bismark_bt2_pe._10x.bedgraph.bed\r\n" ] } ], "source": [ "#Confirm BEDfile creation\n", "!find *.bed" ] }, { "cell_type": "code", "execution_count": 30, "metadata": { "scrolled": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "1\t208521\t208523\r\n", "1\t208524\t208526\r\n", "1\t212911\t212913\r\n", "1\t213160\t213162\r\n", "1\t213207\t213209\r\n", "1\t213247\t213249\r\n", "1\t213252\t213254\r\n", "1\t217269\t217271\r\n", "1\t217349\t217351\r\n", "1\t238052\t238054\r\n" ] } ], "source": [ "#Confirm file creation\n", "!head Meth10_R1_001_val_1_bismark_bt2_pe._10x.bedgraph.bed" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "#### 4b. Genes" ] }, { "cell_type": "code", "execution_count": 49, "metadata": { "collapsed": true, "scrolled": true }, "outputs": [], "source": [ "%%bash\n", "\n", "for f in *bed\n", "do\n", " /usr/local/bin/intersectBed \\\n", " -wb \\\n", " -a ${f} \\\n", " -b ../../../genome-feature-files/Mcap.GFFannotation.gene.gff \\\n", " > ${f}-mcGenes\n", "done" ] }, { "cell_type": "code", "execution_count": 50, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "==> Meth10_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-Meth.bed-mcGenes <==\n", "1\t789544\t789546\t1\tAUGUSTUS\tgene\t789380\t790334\t0.68\t-\t.\tg21600\n", "1\t789590\t789592\t1\tAUGUSTUS\tgene\t789380\t790334\t0.68\t-\t.\tg21600\n", "1\t876587\t876589\t1\tAUGUSTUS\tgene\t875739\t924977\t0.37\t+\t.\tg21603\n", "1\t876606\t876608\t1\tAUGUSTUS\tgene\t875739\t924977\t0.37\t+\t.\tg21603\n", "1\t1267992\t1267994\t1\tAUGUSTUS\tgene\t1234405\t1276748\t0.95\t-\t.\tg21628\n", "1\t1269495\t1269497\t1\tAUGUSTUS\tgene\t1234405\t1276748\t0.95\t-\t.\tg21628\n", "1\t1269508\t1269510\t1\tAUGUSTUS\tgene\t1234405\t1276748\t0.95\t-\t.\tg21628\n", "1\t1269532\t1269534\t1\tAUGUSTUS\tgene\t1234405\t1276748\t0.95\t-\t.\tg21628\n", "1\t1373604\t1373606\t1\tAUGUSTUS\tgene\t1361058\t1381745\t1\t-\t.\tg21633\n", "1\t1387604\t1387606\t1\tAUGUSTUS\tgene\t1385571\t1392430\t1\t+\t.\tg21634\n", "\n", "==> Meth10_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-sparseMeth.bed-mcGenes <==\n", "1\t437346\t437348\t1\tAUGUSTUS\tgene\t435136\t440238\t0.92\t+\t.\tg21564\n", "1\t437349\t437351\t1\tAUGUSTUS\tgene\t435136\t440238\t0.92\t+\t.\tg21564\n", "1\t527701\t527703\t1\tAUGUSTUS\tgene\t524298\t537113\t1\t-\t.\tg21573\n", "1\t527706\t527708\t1\tAUGUSTUS\tgene\t524298\t537113\t1\t-\t.\tg21573\n", "1\t527726\t527728\t1\tAUGUSTUS\tgene\t524298\t537113\t1\t-\t.\tg21573\n", "1\t527739\t527741\t1\tAUGUSTUS\tgene\t524298\t537113\t1\t-\t.\tg21573\n", "1\t624562\t624564\t1\tAUGUSTUS\tgene\t622962\t633865\t0.45\t+\t.\tg21583\n", "1\t789388\t789390\t1\tAUGUSTUS\tgene\t789380\t790334\t0.68\t-\t.\tg21600\n", "1\t789472\t789474\t1\tAUGUSTUS\tgene\t789380\t790334\t0.68\t-\t.\tg21600\n", "1\t789598\t789600\t1\tAUGUSTUS\tgene\t789380\t790334\t0.68\t-\t.\tg21600\n", "\n", "==> Meth10_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-unMeth.bed-mcGenes <==\n", "1\t238052\t238054\t1\tAUGUSTUS\tgene\t237955\t238956\t1\t+\t.\tg21550\n", "1\t238133\t238135\t1\tAUGUSTUS\tgene\t237955\t238956\t1\t+\t.\tg21550\n", "1\t323150\t323152\t1\tAUGUSTUS\tgene\t323002\t331686\t1\t-\t.\tg21554\n", "1\t323157\t323159\t1\tAUGUSTUS\tgene\t323002\t331686\t1\t-\t.\tg21554\n", "1\t323172\t323174\t1\tAUGUSTUS\tgene\t323002\t331686\t1\t-\t.\tg21554\n", "1\t323177\t323179\t1\tAUGUSTUS\tgene\t323002\t331686\t1\t-\t.\tg21554\n", "1\t323190\t323192\t1\tAUGUSTUS\tgene\t323002\t331686\t1\t-\t.\tg21554\n", "1\t323320\t323322\t1\tAUGUSTUS\tgene\t323002\t331686\t1\t-\t.\tg21554\n", "1\t323396\t323398\t1\tAUGUSTUS\tgene\t323002\t331686\t1\t-\t.\tg21554\n", "1\t323429\t323431\t1\tAUGUSTUS\tgene\t323002\t331686\t1\t-\t.\tg21554\n", "\n", "==> Meth10_R1_001_val_1_bismark_bt2_pe._10x.bedgraph.bed-mcGenes <==\n", "1\t238052\t238054\t1\tAUGUSTUS\tgene\t237955\t238956\t1\t+\t.\tg21550\n", "1\t238133\t238135\t1\tAUGUSTUS\tgene\t237955\t238956\t1\t+\t.\tg21550\n", "1\t323150\t323152\t1\tAUGUSTUS\tgene\t323002\t331686\t1\t-\t.\tg21554\n", "1\t323157\t323159\t1\tAUGUSTUS\tgene\t323002\t331686\t1\t-\t.\tg21554\n", "1\t323172\t323174\t1\tAUGUSTUS\tgene\t323002\t331686\t1\t-\t.\tg21554\n", "1\t323177\t323179\t1\tAUGUSTUS\tgene\t323002\t331686\t1\t-\t.\tg21554\n", "1\t323190\t323192\t1\tAUGUSTUS\tgene\t323002\t331686\t1\t-\t.\tg21554\n", "1\t323320\t323322\t1\tAUGUSTUS\tgene\t323002\t331686\t1\t-\t.\tg21554\n", "1\t323396\t323398\t1\tAUGUSTUS\tgene\t323002\t331686\t1\t-\t.\tg21554\n", "1\t323429\t323431\t1\tAUGUSTUS\tgene\t323002\t331686\t1\t-\t.\tg21554\n", "\n", "==> Meth11_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-Meth.bed-mcGenes <==\n", "1\t744619\t744621\t1\tAUGUSTUS\tgene\t743708\t771725\t0.98\t-\t.\tg21595\n", "1\t1264052\t1264054\t1\tAUGUSTUS\tgene\t1234405\t1276748\t0.95\t-\t.\tg21628\n", "1\t1269495\t1269497\t1\tAUGUSTUS\tgene\t1234405\t1276748\t0.95\t-\t.\tg21628\n", "1\t1269508\t1269510\t1\tAUGUSTUS\tgene\t1234405\t1276748\t0.95\t-\t.\tg21628\n", "1\t1269532\t1269534\t1\tAUGUSTUS\tgene\t1234405\t1276748\t0.95\t-\t.\tg21628\n", "1\t1273421\t1273423\t1\tAUGUSTUS\tgene\t1234405\t1276748\t0.95\t-\t.\tg21628\n", "1\t1273455\t1273457\t1\tAUGUSTUS\tgene\t1234405\t1276748\t0.95\t-\t.\tg21628\n", "1\t1273463\t1273465\t1\tAUGUSTUS\tgene\t1234405\t1276748\t0.95\t-\t.\tg21628\n", "1\t1338202\t1338204\t1\tAUGUSTUS\tgene\t1326918\t1338740\t1\t-\t.\tg21630\n", "1\t1338258\t1338260\t1\tAUGUSTUS\tgene\t1326918\t1338740\t1\t-\t.\tg21630\n", "\n", "==> Meth11_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-sparseMeth.bed-mcGenes <==\n", "1\t581543\t581545\t1\tAUGUSTUS\tgene\t581411\t581815\t0.67\t-\t.\tg21577\n", "1\t581570\t581572\t1\tAUGUSTUS\tgene\t581411\t581815\t0.67\t-\t.\tg21577\n", "1\t744050\t744052\t1\tAUGUSTUS\tgene\t743708\t771725\t0.98\t-\t.\tg21595\n", "1\t744608\t744610\t1\tAUGUSTUS\tgene\t743708\t771725\t0.98\t-\t.\tg21595\n", "1\t785550\t785552\t1\tAUGUSTUS\tgene\t784627\t785798\t0.83\t-\t.\tg21597\n", "1\t786094\t786096\t1\tAUGUSTUS\tgene\t785899\t786207\t0.98\t-\t.\tg21598\n", "1\t1131883\t1131885\t1\tAUGUSTUS\tgene\t1121855\t1134134\t0.34\t+\t.\tg21620\n", "1\t1131892\t1131894\t1\tAUGUSTUS\tgene\t1121855\t1134134\t0.34\t+\t.\tg21620\n", "1\t1236857\t1236859\t1\tAUGUSTUS\tgene\t1234405\t1276748\t0.95\t-\t.\tg21628\n", "1\t1236887\t1236889\t1\tAUGUSTUS\tgene\t1234405\t1276748\t0.95\t-\t.\tg21628\n", "\n", "==> Meth11_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-unMeth.bed-mcGenes <==\n", "1\t238620\t238622\t1\tAUGUSTUS\tgene\t237955\t238956\t1\t+\t.\tg21550\n", "1\t323354\t323356\t1\tAUGUSTUS\tgene\t323002\t331686\t1\t-\t.\tg21554\n", "1\t323373\t323375\t1\tAUGUSTUS\tgene\t323002\t331686\t1\t-\t.\tg21554\n", "1\t323396\t323398\t1\tAUGUSTUS\tgene\t323002\t331686\t1\t-\t.\tg21554\n", "1\t323429\t323431\t1\tAUGUSTUS\tgene\t323002\t331686\t1\t-\t.\tg21554\n", "1\t323524\t323526\t1\tAUGUSTUS\tgene\t323002\t331686\t1\t-\t.\tg21554\n", "1\t324840\t324842\t1\tAUGUSTUS\tgene\t323002\t331686\t1\t-\t.\tg21554\n", "1\t324861\t324863\t1\tAUGUSTUS\tgene\t323002\t331686\t1\t-\t.\tg21554\n", "1\t324874\t324876\t1\tAUGUSTUS\tgene\t323002\t331686\t1\t-\t.\tg21554\n", "1\t324876\t324878\t1\tAUGUSTUS\tgene\t323002\t331686\t1\t-\t.\tg21554\n", "\n", "==> Meth11_R1_001_val_1_bismark_bt2_pe._10x.bedgraph.bed-mcGenes <==\n", "1\t238620\t238622\t1\tAUGUSTUS\tgene\t237955\t238956\t1\t+\t.\tg21550\n", "1\t323354\t323356\t1\tAUGUSTUS\tgene\t323002\t331686\t1\t-\t.\tg21554\n", "1\t323373\t323375\t1\tAUGUSTUS\tgene\t323002\t331686\t1\t-\t.\tg21554\n", "1\t323396\t323398\t1\tAUGUSTUS\tgene\t323002\t331686\t1\t-\t.\tg21554\n", "1\t323429\t323431\t1\tAUGUSTUS\tgene\t323002\t331686\t1\t-\t.\tg21554\n", "1\t323524\t323526\t1\tAUGUSTUS\tgene\t323002\t331686\t1\t-\t.\tg21554\n", "1\t324840\t324842\t1\tAUGUSTUS\tgene\t323002\t331686\t1\t-\t.\tg21554\n", "1\t324861\t324863\t1\tAUGUSTUS\tgene\t323002\t331686\t1\t-\t.\tg21554\n", "1\t324874\t324876\t1\tAUGUSTUS\tgene\t323002\t331686\t1\t-\t.\tg21554\n", "1\t324876\t324878\t1\tAUGUSTUS\tgene\t323002\t331686\t1\t-\t.\tg21554\n", "\n", "==> Meth12_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-Meth.bed-mcGenes <==\n", "1\t69151\t69153\t1\tAUGUSTUS\tgene\t64466\t84798\t1\t+\t.\tg21536\n", "1\t69235\t69237\t1\tAUGUSTUS\tgene\t64466\t84798\t1\t+\t.\tg21536\n", "1\t69580\t69582\t1\tAUGUSTUS\tgene\t64466\t84798\t1\t+\t.\tg21536\n", "1\t69584\t69586\t1\tAUGUSTUS\tgene\t64466\t84798\t1\t+\t.\tg21536\n", "1\t69845\t69847\t1\tAUGUSTUS\tgene\t64466\t84798\t1\t+\t.\tg21536\n", "1\t69882\t69884\t1\tAUGUSTUS\tgene\t64466\t84798\t1\t+\t.\tg21536\n", "1\t70019\t70021\t1\tAUGUSTUS\tgene\t64466\t84798\t1\t+\t.\tg21536\n", "1\t70068\t70070\t1\tAUGUSTUS\tgene\t64466\t84798\t1\t+\t.\tg21536\n", "1\t70083\t70085\t1\tAUGUSTUS\tgene\t64466\t84798\t1\t+\t.\tg21536\n", "1\t70129\t70131\t1\tAUGUSTUS\tgene\t64466\t84798\t1\t+\t.\tg21536\n", "\n", "==> Meth12_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-sparseMeth.bed-mcGenes <==\n", "1\t79955\t79957\t1\tAUGUSTUS\tgene\t64466\t84798\t1\t+\t.\tg21536\n", "1\t356393\t356395\t1\tAUGUSTUS\tgene\t353765\t356968\t0.98\t+\t.\tg21557\n", "1\t420896\t420898\t1\tAUGUSTUS\tgene\t420478\t420918\t0.52\t+\t.\tg21562\n", "1\t624754\t624756\t1\tAUGUSTUS\tgene\t622962\t633865\t0.45\t+\t.\tg21583\n", "1\t744671\t744673\t1\tAUGUSTUS\tgene\t743708\t771725\t0.98\t-\t.\tg21595\n", "1\t754293\t754295\t1\tAUGUSTUS\tgene\t743708\t771725\t0.98\t-\t.\tg21595\n", "1\t754314\t754316\t1\tAUGUSTUS\tgene\t743708\t771725\t0.98\t-\t.\tg21595\n", "1\t789590\t789592\t1\tAUGUSTUS\tgene\t789380\t790334\t0.68\t-\t.\tg21600\n", "1\t789598\t789600\t1\tAUGUSTUS\tgene\t789380\t790334\t0.68\t-\t.\tg21600\n", "1\t789613\t789615\t1\tAUGUSTUS\tgene\t789380\t790334\t0.68\t-\t.\tg21600\n", "\n", "==> Meth12_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-unMeth.bed-mcGenes <==\n", "1\t46025\t46027\t1\tAUGUSTUS\tgene\t37447\t52266\t1\t+\t.\tg21534\n", "1\t49087\t49089\t1\tAUGUSTUS\tgene\t37447\t52266\t1\t+\t.\tg21534\n", "1\t49093\t49095\t1\tAUGUSTUS\tgene\t37447\t52266\t1\t+\t.\tg21534\n", "1\t49102\t49104\t1\tAUGUSTUS\tgene\t37447\t52266\t1\t+\t.\tg21534\n", "1\t49119\t49121\t1\tAUGUSTUS\tgene\t37447\t52266\t1\t+\t.\tg21534\n", "1\t49123\t49125\t1\tAUGUSTUS\tgene\t37447\t52266\t1\t+\t.\tg21534\n", "1\t49169\t49171\t1\tAUGUSTUS\tgene\t37447\t52266\t1\t+\t.\tg21534\n", "1\t49194\t49196\t1\tAUGUSTUS\tgene\t37447\t52266\t1\t+\t.\tg21534\n", "1\t75386\t75388\t1\tAUGUSTUS\tgene\t64466\t84798\t1\t+\t.\tg21536\n", "1\t75401\t75403\t1\tAUGUSTUS\tgene\t64466\t84798\t1\t+\t.\tg21536\n", "\n", "==> Meth12_R1_001_val_1_bismark_bt2_pe._10x.bedgraph.bed-mcGenes <==\n", "1\t46025\t46027\t1\tAUGUSTUS\tgene\t37447\t52266\t1\t+\t.\tg21534\n", "1\t49087\t49089\t1\tAUGUSTUS\tgene\t37447\t52266\t1\t+\t.\tg21534\n", "1\t49093\t49095\t1\tAUGUSTUS\tgene\t37447\t52266\t1\t+\t.\tg21534\n", "1\t49102\t49104\t1\tAUGUSTUS\tgene\t37447\t52266\t1\t+\t.\tg21534\n", "1\t49119\t49121\t1\tAUGUSTUS\tgene\t37447\t52266\t1\t+\t.\tg21534\n", "1\t49123\t49125\t1\tAUGUSTUS\tgene\t37447\t52266\t1\t+\t.\tg21534\n", "1\t49169\t49171\t1\tAUGUSTUS\tgene\t37447\t52266\t1\t+\t.\tg21534\n", "1\t49194\t49196\t1\tAUGUSTUS\tgene\t37447\t52266\t1\t+\t.\tg21534\n", "1\t69151\t69153\t1\tAUGUSTUS\tgene\t64466\t84798\t1\t+\t.\tg21536\n", "1\t69235\t69237\t1\tAUGUSTUS\tgene\t64466\t84798\t1\t+\t.\tg21536\n", "\n", "==> Meth13_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-Meth.bed-mcGenes <==\n", "1\t58618\t58620\t1\tAUGUSTUS\tgene\t58322\t62557\t1\t-\t.\tg21535\n", "1\t58745\t58747\t1\tAUGUSTUS\tgene\t58322\t62557\t1\t-\t.\tg21535\n", "1\t58764\t58766\t1\tAUGUSTUS\tgene\t58322\t62557\t1\t-\t.\tg21535\n", "1\t58792\t58794\t1\tAUGUSTUS\tgene\t58322\t62557\t1\t-\t.\tg21535\n", "1\t80721\t80723\t1\tAUGUSTUS\tgene\t64466\t84798\t1\t+\t.\tg21536\n", "1\t101462\t101464\t1\tAUGUSTUS\tgene\t100215\t109729\t0.99\t-\t.\tg21538\n", "1\t101535\t101537\t1\tAUGUSTUS\tgene\t100215\t109729\t0.99\t-\t.\tg21538\n", "1\t108331\t108333\t1\tAUGUSTUS\tgene\t100215\t109729\t0.99\t-\t.\tg21538\n", "1\t108383\t108385\t1\tAUGUSTUS\tgene\t100215\t109729\t0.99\t-\t.\tg21538\n", "1\t108427\t108429\t1\tAUGUSTUS\tgene\t100215\t109729\t0.99\t-\t.\tg21538\n", "\n", "==> Meth13_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-sparseMeth.bed-mcGenes <==\n", "1\t45163\t45165\t1\tAUGUSTUS\tgene\t37447\t52266\t1\t+\t.\tg21534\n", "1\t48370\t48372\t1\tAUGUSTUS\tgene\t37447\t52266\t1\t+\t.\tg21534\n", "1\t332927\t332929\t1\tAUGUSTUS\tgene\t332282\t348965\t0.61\t-\t.\tg21555\n", "1\t336069\t336071\t1\tAUGUSTUS\tgene\t332282\t348965\t0.61\t-\t.\tg21555\n", "1\t336217\t336219\t1\tAUGUSTUS\tgene\t332282\t348965\t0.61\t-\t.\tg21555\n", "1\t349633\t349635\t1\tAUGUSTUS\tgene\t349160\t352265\t0.98\t+\t.\tg21556\n", "1\t369283\t369285\t1\tAUGUSTUS\tgene\t361628\t375371\t0.32\t-\t.\tg21558\n", "1\t369679\t369681\t1\tAUGUSTUS\tgene\t361628\t375371\t0.32\t-\t.\tg21558\n", "1\t372648\t372650\t1\tAUGUSTUS\tgene\t361628\t375371\t0.32\t-\t.\tg21558\n", "1\t526047\t526049\t1\tAUGUSTUS\tgene\t524298\t537113\t1\t-\t.\tg21573\n", "\n", "==> Meth13_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-unMeth.bed-mcGenes <==\n", "1\t22445\t22447\t1\tAUGUSTUS\tgene\t22321\t27293\t0.23\t-\t.\tg21533\n", "1\t22505\t22507\t1\tAUGUSTUS\tgene\t22321\t27293\t0.23\t-\t.\tg21533\n", "1\t22513\t22515\t1\tAUGUSTUS\tgene\t22321\t27293\t0.23\t-\t.\tg21533\n", "1\t22531\t22533\t1\tAUGUSTUS\tgene\t22321\t27293\t0.23\t-\t.\tg21533\n", "1\t22534\t22536\t1\tAUGUSTUS\tgene\t22321\t27293\t0.23\t-\t.\tg21533\n", "1\t22547\t22549\t1\tAUGUSTUS\tgene\t22321\t27293\t0.23\t-\t.\tg21533\n", "1\t22563\t22565\t1\tAUGUSTUS\tgene\t22321\t27293\t0.23\t-\t.\tg21533\n", "1\t23117\t23119\t1\tAUGUSTUS\tgene\t22321\t27293\t0.23\t-\t.\tg21533\n", "1\t23139\t23141\t1\tAUGUSTUS\tgene\t22321\t27293\t0.23\t-\t.\tg21533\n", "1\t23173\t23175\t1\tAUGUSTUS\tgene\t22321\t27293\t0.23\t-\t.\tg21533\n", "\n", "==> Meth13_R1_001_val_1_bismark_bt2_pe._10x.bedgraph.bed-mcGenes <==\n", "1\t22445\t22447\t1\tAUGUSTUS\tgene\t22321\t27293\t0.23\t-\t.\tg21533\n", "1\t22505\t22507\t1\tAUGUSTUS\tgene\t22321\t27293\t0.23\t-\t.\tg21533\n", "1\t22513\t22515\t1\tAUGUSTUS\tgene\t22321\t27293\t0.23\t-\t.\tg21533\n", "1\t22531\t22533\t1\tAUGUSTUS\tgene\t22321\t27293\t0.23\t-\t.\tg21533\n", "1\t22534\t22536\t1\tAUGUSTUS\tgene\t22321\t27293\t0.23\t-\t.\tg21533\n", "1\t22547\t22549\t1\tAUGUSTUS\tgene\t22321\t27293\t0.23\t-\t.\tg21533\n", "1\t22563\t22565\t1\tAUGUSTUS\tgene\t22321\t27293\t0.23\t-\t.\tg21533\n", "1\t23117\t23119\t1\tAUGUSTUS\tgene\t22321\t27293\t0.23\t-\t.\tg21533\n", "1\t23139\t23141\t1\tAUGUSTUS\tgene\t22321\t27293\t0.23\t-\t.\tg21533\n", "1\t23173\t23175\t1\tAUGUSTUS\tgene\t22321\t27293\t0.23\t-\t.\tg21533\n", "\n", "==> Meth14_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-Meth.bed-mcGenes <==\n", "1\t58618\t58620\t1\tAUGUSTUS\tgene\t58322\t62557\t1\t-\t.\tg21535\n", "1\t58745\t58747\t1\tAUGUSTUS\tgene\t58322\t62557\t1\t-\t.\tg21535\n", "1\t58764\t58766\t1\tAUGUSTUS\tgene\t58322\t62557\t1\t-\t.\tg21535\n", "1\t58792\t58794\t1\tAUGUSTUS\tgene\t58322\t62557\t1\t-\t.\tg21535\n", "1\t336217\t336219\t1\tAUGUSTUS\tgene\t332282\t348965\t0.61\t-\t.\tg21555\n", "1\t527701\t527703\t1\tAUGUSTUS\tgene\t524298\t537113\t1\t-\t.\tg21573\n", "1\t759941\t759943\t1\tAUGUSTUS\tgene\t743708\t771725\t0.98\t-\t.\tg21595\n", "1\t759954\t759956\t1\tAUGUSTUS\tgene\t743708\t771725\t0.98\t-\t.\tg21595\n", "1\t759983\t759985\t1\tAUGUSTUS\tgene\t743708\t771725\t0.98\t-\t.\tg21595\n", "1\t759985\t759987\t1\tAUGUSTUS\tgene\t743708\t771725\t0.98\t-\t.\tg21595\n", "\n", "==> Meth14_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-sparseMeth.bed-mcGenes <==\n", "1\t323888\t323890\t1\tAUGUSTUS\tgene\t323002\t331686\t1\t-\t.\tg21554\n", "1\t336069\t336071\t1\tAUGUSTUS\tgene\t332282\t348965\t0.61\t-\t.\tg21555\n", "1\t344217\t344219\t1\tAUGUSTUS\tgene\t332282\t348965\t0.61\t-\t.\tg21555\n", "1\t349633\t349635\t1\tAUGUSTUS\tgene\t349160\t352265\t0.98\t+\t.\tg21556\n", "1\t367234\t367236\t1\tAUGUSTUS\tgene\t361628\t375371\t0.32\t-\t.\tg21558\n", "1\t527706\t527708\t1\tAUGUSTUS\tgene\t524298\t537113\t1\t-\t.\tg21573\n", "1\t527726\t527728\t1\tAUGUSTUS\tgene\t524298\t537113\t1\t-\t.\tg21573\n", "1\t527739\t527741\t1\tAUGUSTUS\tgene\t524298\t537113\t1\t-\t.\tg21573\n", "1\t527799\t527801\t1\tAUGUSTUS\tgene\t524298\t537113\t1\t-\t.\tg21573\n", "1\t587749\t587751\t1\tAUGUSTUS\tgene\t587038\t587776\t0.65\t-\t.\tg21579\n", "\n", "==> Meth14_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-unMeth.bed-mcGenes <==\n", "1\t40450\t40452\t1\tAUGUSTUS\tgene\t37447\t52266\t1\t+\t.\tg21534\n", "1\t40486\t40488\t1\tAUGUSTUS\tgene\t37447\t52266\t1\t+\t.\tg21534\n", "1\t40541\t40543\t1\tAUGUSTUS\tgene\t37447\t52266\t1\t+\t.\tg21534\n", "1\t40552\t40554\t1\tAUGUSTUS\tgene\t37447\t52266\t1\t+\t.\tg21534\n", "1\t40555\t40557\t1\tAUGUSTUS\tgene\t37447\t52266\t1\t+\t.\tg21534\n", "1\t44922\t44924\t1\tAUGUSTUS\tgene\t37447\t52266\t1\t+\t.\tg21534\n", "1\t44942\t44944\t1\tAUGUSTUS\tgene\t37447\t52266\t1\t+\t.\tg21534\n", "1\t44946\t44948\t1\tAUGUSTUS\tgene\t37447\t52266\t1\t+\t.\tg21534\n", "1\t44981\t44983\t1\tAUGUSTUS\tgene\t37447\t52266\t1\t+\t.\tg21534\n", "1\t44991\t44993\t1\tAUGUSTUS\tgene\t37447\t52266\t1\t+\t.\tg21534\n", "\n", "==> Meth14_R1_001_val_1_bismark_bt2_pe._10x.bedgraph.bed-mcGenes <==\n", "1\t40450\t40452\t1\tAUGUSTUS\tgene\t37447\t52266\t1\t+\t.\tg21534\n", "1\t40486\t40488\t1\tAUGUSTUS\tgene\t37447\t52266\t1\t+\t.\tg21534\n", "1\t40541\t40543\t1\tAUGUSTUS\tgene\t37447\t52266\t1\t+\t.\tg21534\n", "1\t40552\t40554\t1\tAUGUSTUS\tgene\t37447\t52266\t1\t+\t.\tg21534\n", "1\t40555\t40557\t1\tAUGUSTUS\tgene\t37447\t52266\t1\t+\t.\tg21534\n", "1\t44922\t44924\t1\tAUGUSTUS\tgene\t37447\t52266\t1\t+\t.\tg21534\n", "1\t44942\t44944\t1\tAUGUSTUS\tgene\t37447\t52266\t1\t+\t.\tg21534\n", "1\t44946\t44948\t1\tAUGUSTUS\tgene\t37447\t52266\t1\t+\t.\tg21534\n", "1\t44981\t44983\t1\tAUGUSTUS\tgene\t37447\t52266\t1\t+\t.\tg21534\n", "1\t44991\t44993\t1\tAUGUSTUS\tgene\t37447\t52266\t1\t+\t.\tg21534\n", "\n", "==> Meth15_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-Meth.bed-mcGenes <==\n", "1\t58618\t58620\t1\tAUGUSTUS\tgene\t58322\t62557\t1\t-\t.\tg21535\n", "1\t58745\t58747\t1\tAUGUSTUS\tgene\t58322\t62557\t1\t-\t.\tg21535\n", "1\t58764\t58766\t1\tAUGUSTUS\tgene\t58322\t62557\t1\t-\t.\tg21535\n", "1\t58792\t58794\t1\tAUGUSTUS\tgene\t58322\t62557\t1\t-\t.\tg21535\n", "1\t101462\t101464\t1\tAUGUSTUS\tgene\t100215\t109729\t0.99\t-\t.\tg21538\n", "1\t101535\t101537\t1\tAUGUSTUS\tgene\t100215\t109729\t0.99\t-\t.\tg21538\n", "1\t108751\t108753\t1\tAUGUSTUS\tgene\t100215\t109729\t0.99\t-\t.\tg21538\n", "1\t108778\t108780\t1\tAUGUSTUS\tgene\t100215\t109729\t0.99\t-\t.\tg21538\n", "1\t108787\t108789\t1\tAUGUSTUS\tgene\t100215\t109729\t0.99\t-\t.\tg21538\n", "1\t108803\t108805\t1\tAUGUSTUS\tgene\t100215\t109729\t0.99\t-\t.\tg21538\n", "\n", "==> Meth15_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-sparseMeth.bed-mcGenes <==\n", "1\t41916\t41918\t1\tAUGUSTUS\tgene\t37447\t52266\t1\t+\t.\tg21534\n", "1\t42261\t42263\t1\tAUGUSTUS\tgene\t37447\t52266\t1\t+\t.\tg21534\n", "1\t101503\t101505\t1\tAUGUSTUS\tgene\t100215\t109729\t0.99\t-\t.\tg21538\n", "1\t101545\t101547\t1\tAUGUSTUS\tgene\t100215\t109729\t0.99\t-\t.\tg21538\n", "1\t332804\t332806\t1\tAUGUSTUS\tgene\t332282\t348965\t0.61\t-\t.\tg21555\n", "1\t336069\t336071\t1\tAUGUSTUS\tgene\t332282\t348965\t0.61\t-\t.\tg21555\n", "1\t336217\t336219\t1\tAUGUSTUS\tgene\t332282\t348965\t0.61\t-\t.\tg21555\n", "1\t370881\t370883\t1\tAUGUSTUS\tgene\t361628\t375371\t0.32\t-\t.\tg21558\n", "1\t370967\t370969\t1\tAUGUSTUS\tgene\t361628\t375371\t0.32\t-\t.\tg21558\n", "1\t527706\t527708\t1\tAUGUSTUS\tgene\t524298\t537113\t1\t-\t.\tg21573\n", "\n", "==> Meth15_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-unMeth.bed-mcGenes <==\n", "1\t40450\t40452\t1\tAUGUSTUS\tgene\t37447\t52266\t1\t+\t.\tg21534\n", "1\t40486\t40488\t1\tAUGUSTUS\tgene\t37447\t52266\t1\t+\t.\tg21534\n", "1\t40541\t40543\t1\tAUGUSTUS\tgene\t37447\t52266\t1\t+\t.\tg21534\n", "1\t40552\t40554\t1\tAUGUSTUS\tgene\t37447\t52266\t1\t+\t.\tg21534\n", "1\t40555\t40557\t1\tAUGUSTUS\tgene\t37447\t52266\t1\t+\t.\tg21534\n", "1\t41832\t41834\t1\tAUGUSTUS\tgene\t37447\t52266\t1\t+\t.\tg21534\n", "1\t41845\t41847\t1\tAUGUSTUS\tgene\t37447\t52266\t1\t+\t.\tg21534\n", "1\t41864\t41866\t1\tAUGUSTUS\tgene\t37447\t52266\t1\t+\t.\tg21534\n", "1\t41974\t41976\t1\tAUGUSTUS\tgene\t37447\t52266\t1\t+\t.\tg21534\n", "1\t42117\t42119\t1\tAUGUSTUS\tgene\t37447\t52266\t1\t+\t.\tg21534\n", "\n", "==> Meth15_R1_001_val_1_bismark_bt2_pe._10x.bedgraph.bed-mcGenes <==\n", "1\t40450\t40452\t1\tAUGUSTUS\tgene\t37447\t52266\t1\t+\t.\tg21534\n", "1\t40486\t40488\t1\tAUGUSTUS\tgene\t37447\t52266\t1\t+\t.\tg21534\n", "1\t40541\t40543\t1\tAUGUSTUS\tgene\t37447\t52266\t1\t+\t.\tg21534\n", "1\t40552\t40554\t1\tAUGUSTUS\tgene\t37447\t52266\t1\t+\t.\tg21534\n", "1\t40555\t40557\t1\tAUGUSTUS\tgene\t37447\t52266\t1\t+\t.\tg21534\n", "1\t41832\t41834\t1\tAUGUSTUS\tgene\t37447\t52266\t1\t+\t.\tg21534\n", "1\t41845\t41847\t1\tAUGUSTUS\tgene\t37447\t52266\t1\t+\t.\tg21534\n", "1\t41864\t41866\t1\tAUGUSTUS\tgene\t37447\t52266\t1\t+\t.\tg21534\n", "1\t41916\t41918\t1\tAUGUSTUS\tgene\t37447\t52266\t1\t+\t.\tg21534\n", "1\t41974\t41976\t1\tAUGUSTUS\tgene\t37447\t52266\t1\t+\t.\tg21534\n", "\n", "==> Meth16_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-Meth.bed-mcGenes <==\n", "1\t1536523\t1536525\t1\tAUGUSTUS\tgene\t1515644\t1593061\t0.76\t+\t.\tg21645\n", "1\t1536643\t1536645\t1\tAUGUSTUS\tgene\t1515644\t1593061\t0.76\t+\t.\tg21645\n", "1\t1536657\t1536659\t1\tAUGUSTUS\tgene\t1515644\t1593061\t0.76\t+\t.\tg21645\n", "1\t1755684\t1755686\t1\tAUGUSTUS\tgene\t1749946\t1765665\t0.92\t-\t.\tg21659\n", "1\t1958635\t1958637\t1\tAUGUSTUS\tgene\t1953301\t1968254\t0.99\t+\t.\tg21683\n", "1\t1958667\t1958669\t1\tAUGUSTUS\tgene\t1953301\t1968254\t0.99\t+\t.\tg21683\n", "1\t1958693\t1958695\t1\tAUGUSTUS\tgene\t1953301\t1968254\t0.99\t+\t.\tg21683\n", "1\t1958702\t1958704\t1\tAUGUSTUS\tgene\t1953301\t1968254\t0.99\t+\t.\tg21683\n", "1\t2264832\t2264834\t1\tAUGUSTUS\tgene\t2256857\t2267938\t0.65\t-\t.\tg21703\n", "1\t2264871\t2264873\t1\tAUGUSTUS\tgene\t2256857\t2267938\t0.65\t-\t.\tg21703\n", "\n", "==> Meth16_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-sparseMeth.bed-mcGenes <==\n", "1\t1540374\t1540376\t1\tAUGUSTUS\tgene\t1515644\t1593061\t0.76\t+\t.\tg21645\n", "2\t1704675\t1704677\t2\tAUGUSTUS\tgene\t1704290\t1704742\t0.58\t-\t.\tg21949\n", "2\t1704686\t1704688\t2\tAUGUSTUS\tgene\t1704290\t1704742\t0.58\t-\t.\tg21949\n", "2\t1704736\t1704738\t2\tAUGUSTUS\tgene\t1704290\t1704742\t0.58\t-\t.\tg21949\n", "2\t1984257\t1984259\t2\tAUGUSTUS\tgene\t1983612\t1984774\t0.57\t-\t.\tg21974\n", "4\t415651\t415653\t4\tAUGUSTUS\tgene\t402886\t416463\t0.54\t+\t.\tg22307\n", "4\t415664\t415666\t4\tAUGUSTUS\tgene\t402886\t416463\t0.54\t+\t.\tg22307\n", "4\t1848309\t1848311\t4\tAUGUSTUS\tgene\t1846639\t1852836\t1\t-\t.\tg22401\n", "6\t1212933\t1212935\t6\tAUGUSTUS\tgene\t1211568\t1217188\t1\t-\t.\tg22753\n", "6\t1212942\t1212944\t6\tAUGUSTUS\tgene\t1211568\t1217188\t1\t-\t.\tg22753\n", "\n", "==> Meth16_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-unMeth.bed-mcGenes <==\n", "1\t2311899\t2311901\t1\tAUGUSTUS\tgene\t2311594\t2345468\t1\t-\t.\tg21705\n", "1\t2311908\t2311910\t1\tAUGUSTUS\tgene\t2311594\t2345468\t1\t-\t.\tg21705\n", "1\t2907968\t2907970\t1\tAUGUSTUS\tgene\t2902908\t2918764\t1\t+\t.\tg21743\n", "2\t773507\t773509\t2\tAUGUSTUS\tgene\t769271\t777949\t1\t+\t.\tg21893\n", "2\t1984223\t1984225\t2\tAUGUSTUS\tgene\t1983612\t1984774\t0.57\t-\t.\tg21974\n", "4\t415666\t415668\t4\tAUGUSTUS\tgene\t402886\t416463\t0.54\t+\t.\tg22307\n", "4\t901529\t901531\t4\tAUGUSTUS\tgene\t900901\t902022\t1\t+\t.\tg22337\n", "4\t901536\t901538\t4\tAUGUSTUS\tgene\t900901\t902022\t1\t+\t.\tg22337\n", "4\t901541\t901543\t4\tAUGUSTUS\tgene\t900901\t902022\t1\t+\t.\tg22337\n", "4\t1631207\t1631209\t4\tAUGUSTUS\tgene\t1626169\t1631441\t0.37\t+\t.\tg22385\n", "\n", "==> Meth16_R1_001_val_1_bismark_bt2_pe._10x.bedgraph.bed-mcGenes <==\n", "1\t1536523\t1536525\t1\tAUGUSTUS\tgene\t1515644\t1593061\t0.76\t+\t.\tg21645\n", "1\t1536643\t1536645\t1\tAUGUSTUS\tgene\t1515644\t1593061\t0.76\t+\t.\tg21645\n", "1\t1536657\t1536659\t1\tAUGUSTUS\tgene\t1515644\t1593061\t0.76\t+\t.\tg21645\n", "1\t1540374\t1540376\t1\tAUGUSTUS\tgene\t1515644\t1593061\t0.76\t+\t.\tg21645\n", "1\t1755684\t1755686\t1\tAUGUSTUS\tgene\t1749946\t1765665\t0.92\t-\t.\tg21659\n", "1\t1958635\t1958637\t1\tAUGUSTUS\tgene\t1953301\t1968254\t0.99\t+\t.\tg21683\n", "1\t1958667\t1958669\t1\tAUGUSTUS\tgene\t1953301\t1968254\t0.99\t+\t.\tg21683\n", "1\t1958693\t1958695\t1\tAUGUSTUS\tgene\t1953301\t1968254\t0.99\t+\t.\tg21683\n", "1\t1958702\t1958704\t1\tAUGUSTUS\tgene\t1953301\t1968254\t0.99\t+\t.\tg21683\n", "1\t2264832\t2264834\t1\tAUGUSTUS\tgene\t2256857\t2267938\t0.65\t-\t.\tg21703\n", "\n", "==> Meth17_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-Meth.bed-mcGenes <==\n", "1\t1987244\t1987246\t1\tAUGUSTUS\tgene\t1984567\t2003518\t0.99\t+\t.\tg21685\n", "1\t1987263\t1987265\t1\tAUGUSTUS\tgene\t1984567\t2003518\t0.99\t+\t.\tg21685\n", "2\t3037511\t3037513\t2\tAUGUSTUS\tgene\t3037241\t3037690\t1\t-\t.\tg22169\n", "2\t3037528\t3037530\t2\tAUGUSTUS\tgene\t3037241\t3037690\t1\t-\t.\tg22169\n", "6\t2128294\t2128296\t6\tAUGUSTUS\tgene\t2125022\t2129718\t0.58\t-\t.\tg22812\n", "6\t2128304\t2128306\t6\tAUGUSTUS\tgene\t2125022\t2129718\t0.58\t-\t.\tg22812\n", "6\t2128347\t2128349\t6\tAUGUSTUS\tgene\t2125022\t2129718\t0.58\t-\t.\tg22812\n", "6\t2130423\t2130425\t6\tAUGUSTUS\tgene\t2129874\t2130850\t0.47\t-\t.\tg22813\n", "6\t2130432\t2130434\t6\tAUGUSTUS\tgene\t2129874\t2130850\t0.47\t-\t.\tg22813\n", "6\t2130436\t2130438\t6\tAUGUSTUS\tgene\t2129874\t2130850\t0.47\t-\t.\tg22813\n", "\n", "==> Meth17_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-sparseMeth.bed-mcGenes <==\n", "4\t811595\t811597\t4\tAUGUSTUS\tgene\t784630\t817728\t1\t-\t.\tg22330\n", "4\t811607\t811609\t4\tAUGUSTUS\tgene\t784630\t817728\t1\t-\t.\tg22330\n", "6\t2130399\t2130401\t6\tAUGUSTUS\tgene\t2129874\t2130850\t0.47\t-\t.\tg22813\n", "6\t2130495\t2130497\t6\tAUGUSTUS\tgene\t2129874\t2130850\t0.47\t-\t.\tg22813\n", "6\t2130504\t2130506\t6\tAUGUSTUS\tgene\t2129874\t2130850\t0.47\t-\t.\tg22813\n", "7\t1957296\t1957298\t7\tAUGUSTUS\tgene\t1948122\t1976462\t0.84\t-\t.\tg23037\n", "7\t1957322\t1957324\t7\tAUGUSTUS\tgene\t1948122\t1976462\t0.84\t-\t.\tg23037\n", "9\t23708\t23710\t9\tAUGUSTUS\tgene\t23704\t24276\t1\t+\t.\tg23074\n", "9\t23768\t23770\t9\tAUGUSTUS\tgene\t23704\t24276\t1\t+\t.\tg23074\n", "9\t23821\t23823\t9\tAUGUSTUS\tgene\t23704\t24276\t1\t+\t.\tg23074\n", "\n", "==> Meth17_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-unMeth.bed-mcGenes <==\n", "1\t832598\t832600\t1\tAUGUSTUS\tgene\t820948\t851855\t0.36\t-\t.\tg21601\n", "1\t2608371\t2608373\t1\tAUGUSTUS\tgene\t2548946\t2617412\t0.39\t+\t.\tg21721\n", "4\t811590\t811592\t4\tAUGUSTUS\tgene\t784630\t817728\t1\t-\t.\tg22330\n", "4\t1192766\t1192768\t4\tAUGUSTUS\tgene\t1187854\t1193900\t0.92\t+\t.\tg22353\n", "4\t2291584\t2291586\t4\tAUGUSTUS\tgene\t2287083\t2295982\t0.49\t+\t.\tg22430\n", "4\t2291603\t2291605\t4\tAUGUSTUS\tgene\t2287083\t2295982\t0.49\t+\t.\tg22430\n", "4\t2291633\t2291635\t4\tAUGUSTUS\tgene\t2287083\t2295982\t0.49\t+\t.\tg22430\n", "4\t2291699\t2291701\t4\tAUGUSTUS\tgene\t2287083\t2295982\t0.49\t+\t.\tg22430\n", "4\t2291722\t2291724\t4\tAUGUSTUS\tgene\t2287083\t2295982\t0.49\t+\t.\tg22430\n", "4\t2291750\t2291752\t4\tAUGUSTUS\tgene\t2287083\t2295982\t0.49\t+\t.\tg22430\n", "\n", "==> Meth17_R1_001_val_1_bismark_bt2_pe._10x.bedgraph.bed-mcGenes <==\n", "1\t832598\t832600\t1\tAUGUSTUS\tgene\t820948\t851855\t0.36\t-\t.\tg21601\n", "1\t1987244\t1987246\t1\tAUGUSTUS\tgene\t1984567\t2003518\t0.99\t+\t.\tg21685\n", "1\t1987263\t1987265\t1\tAUGUSTUS\tgene\t1984567\t2003518\t0.99\t+\t.\tg21685\n", "1\t2608371\t2608373\t1\tAUGUSTUS\tgene\t2548946\t2617412\t0.39\t+\t.\tg21721\n", "2\t3037511\t3037513\t2\tAUGUSTUS\tgene\t3037241\t3037690\t1\t-\t.\tg22169\n", "2\t3037528\t3037530\t2\tAUGUSTUS\tgene\t3037241\t3037690\t1\t-\t.\tg22169\n", "4\t811590\t811592\t4\tAUGUSTUS\tgene\t784630\t817728\t1\t-\t.\tg22330\n", "4\t811595\t811597\t4\tAUGUSTUS\tgene\t784630\t817728\t1\t-\t.\tg22330\n", "4\t811607\t811609\t4\tAUGUSTUS\tgene\t784630\t817728\t1\t-\t.\tg22330\n", "4\t1192766\t1192768\t4\tAUGUSTUS\tgene\t1187854\t1193900\t0.92\t+\t.\tg22353\n", "\n", "==> Meth18_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-Meth.bed-mcGenes <==\n", "1\t3129772\t3129774\t1\tAUGUSTUS\tgene\t3125992\t3152597\t0.79\t+\t.\tg21754\n", "1\t3129793\t3129795\t1\tAUGUSTUS\tgene\t3125992\t3152597\t0.79\t+\t.\tg21754\n", "1\t3129805\t3129807\t1\tAUGUSTUS\tgene\t3125992\t3152597\t0.79\t+\t.\tg21754\n", "6\t2130678\t2130680\t6\tAUGUSTUS\tgene\t2129874\t2130850\t0.47\t-\t.\tg22813\n", "6\t2130702\t2130704\t6\tAUGUSTUS\tgene\t2129874\t2130850\t0.47\t-\t.\tg22813\n", "6\t2130774\t2130776\t6\tAUGUSTUS\tgene\t2129874\t2130850\t0.47\t-\t.\tg22813\n", "10\t733001\t733003\t10\tAUGUSTUS\tgene\t732999\t737162\t0.71\t-\t.\tg23342\n", "10\t733024\t733026\t10\tAUGUSTUS\tgene\t732999\t737162\t0.71\t-\t.\tg23342\n", "10\t733030\t733032\t10\tAUGUSTUS\tgene\t732999\t737162\t0.71\t-\t.\tg23342\n", "10\t733037\t733039\t10\tAUGUSTUS\tgene\t732999\t737162\t0.71\t-\t.\tg23342\n", "\n", "==> Meth18_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-sparseMeth.bed-mcGenes <==\n", "7\t86796\t86798\t7\tAUGUSTUS\tgene\t85016\t92846\t0.47\t+\t.\tg22864\n", "18\t1159899\t1159901\t18\tAUGUSTUS\tgene\t1159295\t1167458\t0.42\t+\t.\tg24521\n", "18\t1472691\t1472693\t18\tAUGUSTUS\tgene\t1472674\t1485912\t0.64\t+\t.\tg24547\n", "18\t1472704\t1472706\t18\tAUGUSTUS\tgene\t1472674\t1485912\t0.64\t+\t.\tg24547\n", "18\t1472710\t1472712\t18\tAUGUSTUS\tgene\t1472674\t1485912\t0.64\t+\t.\tg24547\n", "18\t1472714\t1472716\t18\tAUGUSTUS\tgene\t1472674\t1485912\t0.64\t+\t.\tg24547\n", "21\t1326374\t1326376\t21\tAUGUSTUS\tgene\t1291766\t1329764\t0.13\t-\t.\tg25222\n", "21\t1329413\t1329415\t21\tAUGUSTUS\tgene\t1291766\t1329764\t0.13\t-\t.\tg25222\n", "24\t1663542\t1663544\t24\tAUGUSTUS\tgene\t1636109\t1686902\t0.46\t-\t.\tg25540\n", "24\t1663878\t1663880\t24\tAUGUSTUS\tgene\t1636109\t1686902\t0.46\t-\t.\tg25540\n", "\n", "==> Meth18_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-unMeth.bed-mcGenes <==\n", "4\t1572709\t1572711\t4\tAUGUSTUS\tgene\t1571070\t1574805\t0.49\t-\t.\tg22382\n", "4\t1572728\t1572730\t4\tAUGUSTUS\tgene\t1571070\t1574805\t0.49\t-\t.\tg22382\n", "4\t2291584\t2291586\t4\tAUGUSTUS\tgene\t2287083\t2295982\t0.49\t+\t.\tg22430\n", "4\t2291603\t2291605\t4\tAUGUSTUS\tgene\t2287083\t2295982\t0.49\t+\t.\tg22430\n", "4\t2291633\t2291635\t4\tAUGUSTUS\tgene\t2287083\t2295982\t0.49\t+\t.\tg22430\n", "4\t2291699\t2291701\t4\tAUGUSTUS\tgene\t2287083\t2295982\t0.49\t+\t.\tg22430\n", "4\t2291722\t2291724\t4\tAUGUSTUS\tgene\t2287083\t2295982\t0.49\t+\t.\tg22430\n", "4\t2291750\t2291752\t4\tAUGUSTUS\tgene\t2287083\t2295982\t0.49\t+\t.\tg22430\n", "4\t2291757\t2291759\t4\tAUGUSTUS\tgene\t2287083\t2295982\t0.49\t+\t.\tg22430\n", "4\t2291759\t2291761\t4\tAUGUSTUS\tgene\t2287083\t2295982\t0.49\t+\t.\tg22430\n", "\n", "==> Meth18_R1_001_val_1_bismark_bt2_pe._10x.bedgraph.bed-mcGenes <==\n", "1\t3129772\t3129774\t1\tAUGUSTUS\tgene\t3125992\t3152597\t0.79\t+\t.\tg21754\n", "1\t3129793\t3129795\t1\tAUGUSTUS\tgene\t3125992\t3152597\t0.79\t+\t.\tg21754\n", "1\t3129805\t3129807\t1\tAUGUSTUS\tgene\t3125992\t3152597\t0.79\t+\t.\tg21754\n", "4\t1572709\t1572711\t4\tAUGUSTUS\tgene\t1571070\t1574805\t0.49\t-\t.\tg22382\n", "4\t1572728\t1572730\t4\tAUGUSTUS\tgene\t1571070\t1574805\t0.49\t-\t.\tg22382\n", "4\t2291584\t2291586\t4\tAUGUSTUS\tgene\t2287083\t2295982\t0.49\t+\t.\tg22430\n", "4\t2291603\t2291605\t4\tAUGUSTUS\tgene\t2287083\t2295982\t0.49\t+\t.\tg22430\n", "4\t2291633\t2291635\t4\tAUGUSTUS\tgene\t2287083\t2295982\t0.49\t+\t.\tg22430\n", "4\t2291699\t2291701\t4\tAUGUSTUS\tgene\t2287083\t2295982\t0.49\t+\t.\tg22430\n", "4\t2291722\t2291724\t4\tAUGUSTUS\tgene\t2287083\t2295982\t0.49\t+\t.\tg22430\n" ] } ], "source": [ "#Check output\n", "!head *mcGenes" ] }, { "cell_type": "code", "execution_count": 51, "metadata": { "scrolled": true }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ " 17007 Meth10_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-Meth.bed-mcGenes\n", " 15647 Meth10_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-sparseMeth.bed-mcGenes\n", " 127448 Meth10_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-unMeth.bed-mcGenes\n", " 160102 Meth10_R1_001_val_1_bismark_bt2_pe._10x.bedgraph.bed-mcGenes\n", " 23163 Meth11_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-Meth.bed-mcGenes\n", " 15042 Meth11_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-sparseMeth.bed-mcGenes\n", " 128305 Meth11_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-unMeth.bed-mcGenes\n", " 166510 Meth11_R1_001_val_1_bismark_bt2_pe._10x.bedgraph.bed-mcGenes\n", " 82744 Meth12_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-Meth.bed-mcGenes\n", " 44107 Meth12_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-sparseMeth.bed-mcGenes\n", " 507401 Meth12_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-unMeth.bed-mcGenes\n", " 634252 Meth12_R1_001_val_1_bismark_bt2_pe._10x.bedgraph.bed-mcGenes\n", " 99753 Meth13_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-Meth.bed-mcGenes\n", " 46167 Meth13_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-sparseMeth.bed-mcGenes\n", " 842938 Meth13_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-unMeth.bed-mcGenes\n", " 988858 Meth13_R1_001_val_1_bismark_bt2_pe._10x.bedgraph.bed-mcGenes\n", " 67014 Meth14_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-Meth.bed-mcGenes\n", " 39102 Meth14_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-sparseMeth.bed-mcGenes\n", " 674602 Meth14_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-unMeth.bed-mcGenes\n", " 780718 Meth14_R1_001_val_1_bismark_bt2_pe._10x.bedgraph.bed-mcGenes\n", " 86291 Meth15_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-Meth.bed-mcGenes\n", " 53429 Meth15_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-sparseMeth.bed-mcGenes\n", " 825210 Meth15_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-unMeth.bed-mcGenes\n", " 964930 Meth15_R1_001_val_1_bismark_bt2_pe._10x.bedgraph.bed-mcGenes\n", " 6390 Meth16_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-Meth.bed-mcGenes\n", " 1215 Meth16_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-sparseMeth.bed-mcGenes\n", " 3894 Meth16_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-unMeth.bed-mcGenes\n", " 11499 Meth16_R1_001_val_1_bismark_bt2_pe._10x.bedgraph.bed-mcGenes\n", " 2373 Meth17_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-Meth.bed-mcGenes\n", " 511 Meth17_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-sparseMeth.bed-mcGenes\n", " 2243 Meth17_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-unMeth.bed-mcGenes\n", " 5127 Meth17_R1_001_val_1_bismark_bt2_pe._10x.bedgraph.bed-mcGenes\n", " 2018 Meth18_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-Meth.bed-mcGenes\n", " 165 Meth18_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-sparseMeth.bed-mcGenes\n", " 1095 Meth18_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-unMeth.bed-mcGenes\n", " 3278 Meth18_R1_001_val_1_bismark_bt2_pe._10x.bedgraph.bed-mcGenes\n", " 7430548 total\n" ] } ], "source": [ "#Count number of overlaps\n", "!wc -l *mcGenes" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "#### 4c. Coding Sequences (CDS)" ] }, { "cell_type": "code", "execution_count": 52, "metadata": { "collapsed": true, "scrolled": true }, "outputs": [], "source": [ "%%bash\n", "\n", "for f in *bed\n", "do\n", " /usr/local/bin/intersectBed \\\n", " -wb \\\n", " -a ${f} \\\n", " -b ../../../genome-feature-files/Mcap.GFFannotation.CDS.gff \\\n", " > ${f}-mcCDS\n", "done" ] }, { "cell_type": "code", "execution_count": 53, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "==> Meth10_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-Meth.bed-mcCDS <==\r\n", "1\t789544\t789546\t1\tAUGUSTUS\tCDS\t789380\t789726\t0.68\t-\t2\ttranscript_id \"g21600.t1\"; gene_id \"g21600\";\r\n", "1\t789590\t789592\t1\tAUGUSTUS\tCDS\t789380\t789726\t0.68\t-\t2\ttranscript_id \"g21600.t1\"; gene_id \"g21600\";\r\n", "1\t1390109\t1390111\t1\tAUGUSTUS\tCDS\t1390067\t1390192\t1\t+\t0\ttranscript_id \"g21634.t1\"; gene_id \"g21634\";\r\n", "1\t1409734\t1409736\t1\tAUGUSTUS\tCDS\t1409580\t1409782\t1\t-\t2\ttranscript_id \"g21635.t1\"; gene_id \"g21635\";\r\n", "1\t1409778\t1409780\t1\tAUGUSTUS\tCDS\t1409580\t1409782\t1\t-\t2\ttranscript_id \"g21635.t1\"; gene_id \"g21635\";\r\n", "1\t1425319\t1425321\t1\tAUGUSTUS\tCDS\t1425203\t1425363\t1\t+\t2\ttranscript_id \"g21636.t1\"; gene_id \"g21636\";\r\n", "1\t1556613\t1556615\t1\tAUGUSTUS\tCDS\t1556557\t1556755\t1\t+\t0\ttranscript_id \"g21645.t1\"; gene_id \"g21645\";\r\n", "1\t1835566\t1835568\t1\tAUGUSTUS\tCDS\t1835411\t1835679\t1\t+\t2\ttranscript_id \"g21667.t1\"; gene_id \"g21667\";\r\n", "1\t1851774\t1851776\t1\tAUGUSTUS\tCDS\t1851564\t1852055\t1\t-\t0\ttranscript_id \"g21670.t1\"; gene_id \"g21670\";\r\n", "1\t1851897\t1851899\t1\tAUGUSTUS\tCDS\t1851564\t1852055\t1\t-\t0\ttranscript_id \"g21670.t1\"; gene_id \"g21670\";\r\n", "\r\n", "==> Meth10_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-sparseMeth.bed-mcCDS <==\r\n", "1\t437346\t437348\t1\tAUGUSTUS\tCDS\t437225\t437763\t1\t+\t2\ttranscript_id \"g21564.t1\"; gene_id \"g21564\";\r\n", "1\t437349\t437351\t1\tAUGUSTUS\tCDS\t437225\t437763\t1\t+\t2\ttranscript_id \"g21564.t1\"; gene_id \"g21564\";\r\n", "1\t789388\t789390\t1\tAUGUSTUS\tCDS\t789380\t789726\t0.68\t-\t2\ttranscript_id \"g21600.t1\"; gene_id \"g21600\";\r\n", "1\t789472\t789474\t1\tAUGUSTUS\tCDS\t789380\t789726\t0.68\t-\t2\ttranscript_id \"g21600.t1\"; gene_id \"g21600\";\r\n", "1\t789598\t789600\t1\tAUGUSTUS\tCDS\t789380\t789726\t0.68\t-\t2\ttranscript_id \"g21600.t1\"; gene_id \"g21600\";\r\n", "1\t789613\t789615\t1\tAUGUSTUS\tCDS\t789380\t789726\t0.68\t-\t2\ttranscript_id \"g21600.t1\"; gene_id \"g21600\";\r\n", "1\t789648\t789650\t1\tAUGUSTUS\tCDS\t789380\t789726\t0.68\t-\t2\ttranscript_id \"g21600.t1\"; gene_id \"g21600\";\r\n", "1\t789673\t789675\t1\tAUGUSTUS\tCDS\t789380\t789726\t0.68\t-\t2\ttranscript_id \"g21600.t1\"; gene_id \"g21600\";\r\n", "1\t789690\t789692\t1\tAUGUSTUS\tCDS\t789380\t789726\t0.68\t-\t2\ttranscript_id \"g21600.t1\"; gene_id \"g21600\";\r\n", "1\t789693\t789695\t1\tAUGUSTUS\tCDS\t789380\t789726\t0.68\t-\t2\ttranscript_id \"g21600.t1\"; gene_id \"g21600\";\r\n", "\r\n", "==> Meth10_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-unMeth.bed-mcCDS <==\r\n", "1\t238052\t238054\t1\tAUGUSTUS\tCDS\t237955\t238956\t1\t+\t0\ttranscript_id \"g21550.t1\"; gene_id \"g21550\";\r\n", "1\t238133\t238135\t1\tAUGUSTUS\tCDS\t237955\t238956\t1\t+\t0\ttranscript_id \"g21550.t1\"; gene_id \"g21550\";\r\n", "1\t361830\t361832\t1\tAUGUSTUS\tCDS\t361628\t363571\t0.97\t-\t0\ttranscript_id \"g21558.t1\"; gene_id \"g21558\";\r\n", "1\t370608\t370610\t1\tAUGUSTUS\tCDS\t370581\t370722\t1\t-\t2\ttranscript_id \"g21558.t1\"; gene_id \"g21558\";\r\n", "1\t437342\t437344\t1\tAUGUSTUS\tCDS\t437225\t437763\t1\t+\t2\ttranscript_id \"g21564.t1\"; gene_id \"g21564\";\r\n", "1\t437406\t437408\t1\tAUGUSTUS\tCDS\t437225\t437763\t1\t+\t2\ttranscript_id \"g21564.t1\"; gene_id \"g21564\";\r\n", "1\t437466\t437468\t1\tAUGUSTUS\tCDS\t437225\t437763\t1\t+\t2\ttranscript_id \"g21564.t1\"; gene_id \"g21564\";\r\n", "1\t459197\t459199\t1\tAUGUSTUS\tCDS\t459012\t459386\t0.87\t-\t0\ttranscript_id \"g21567.t1\"; gene_id \"g21567\";\r\n", "1\t459225\t459227\t1\tAUGUSTUS\tCDS\t459012\t459386\t0.87\t-\t0\ttranscript_id \"g21567.t1\"; gene_id \"g21567\";\r\n", "1\t524560\t524562\t1\tAUGUSTUS\tCDS\t524298\t526199\t1\t-\t0\ttranscript_id \"g21573.t1\"; gene_id \"g21573\";\r\n", "\r\n", "==> Meth10_R1_001_val_1_bismark_bt2_pe._10x.bedgraph.bed-mcCDS <==\r\n", "1\t238052\t238054\t1\tAUGUSTUS\tCDS\t237955\t238956\t1\t+\t0\ttranscript_id \"g21550.t1\"; gene_id \"g21550\";\r\n", "1\t238133\t238135\t1\tAUGUSTUS\tCDS\t237955\t238956\t1\t+\t0\ttranscript_id \"g21550.t1\"; gene_id \"g21550\";\r\n", "1\t361830\t361832\t1\tAUGUSTUS\tCDS\t361628\t363571\t0.97\t-\t0\ttranscript_id \"g21558.t1\"; gene_id \"g21558\";\r\n", "1\t370608\t370610\t1\tAUGUSTUS\tCDS\t370581\t370722\t1\t-\t2\ttranscript_id \"g21558.t1\"; gene_id \"g21558\";\r\n", "1\t437342\t437344\t1\tAUGUSTUS\tCDS\t437225\t437763\t1\t+\t2\ttranscript_id \"g21564.t1\"; gene_id \"g21564\";\r\n", "1\t437346\t437348\t1\tAUGUSTUS\tCDS\t437225\t437763\t1\t+\t2\ttranscript_id \"g21564.t1\"; gene_id \"g21564\";\r\n", "1\t437349\t437351\t1\tAUGUSTUS\tCDS\t437225\t437763\t1\t+\t2\ttranscript_id \"g21564.t1\"; gene_id \"g21564\";\r\n", "1\t437406\t437408\t1\tAUGUSTUS\tCDS\t437225\t437763\t1\t+\t2\ttranscript_id \"g21564.t1\"; gene_id \"g21564\";\r\n", "1\t437466\t437468\t1\tAUGUSTUS\tCDS\t437225\t437763\t1\t+\t2\ttranscript_id \"g21564.t1\"; gene_id \"g21564\";\r\n", "1\t459197\t459199\t1\tAUGUSTUS\tCDS\t459012\t459386\t0.87\t-\t0\ttranscript_id \"g21567.t1\"; gene_id \"g21567\";\r\n", "\r\n", "==> Meth11_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-Meth.bed-mcCDS <==\r\n", "1\t744619\t744621\t1\tAUGUSTUS\tCDS\t743708\t745054\t0.98\t-\t0\ttranscript_id \"g21595.t1\"; gene_id \"g21595\";\r\n", "1\t1264052\t1264054\t1\tAUGUSTUS\tCDS\t1262915\t1264300\t1\t-\t0\ttranscript_id \"g21628.t1\"; gene_id \"g21628\";\r\n", "1\t1409734\t1409736\t1\tAUGUSTUS\tCDS\t1409580\t1409782\t1\t-\t2\ttranscript_id \"g21635.t1\"; gene_id \"g21635\";\r\n", "1\t1409754\t1409756\t1\tAUGUSTUS\tCDS\t1409580\t1409782\t1\t-\t2\ttranscript_id \"g21635.t1\"; gene_id \"g21635\";\r\n", "1\t1409778\t1409780\t1\tAUGUSTUS\tCDS\t1409580\t1409782\t1\t-\t2\ttranscript_id \"g21635.t1\"; gene_id \"g21635\";\r\n", "1\t1530591\t1530593\t1\tAUGUSTUS\tCDS\t1530584\t1530712\t1\t+\t2\ttranscript_id \"g21645.t1\"; gene_id \"g21645\";\r\n", "1\t1642295\t1642297\t1\tAUGUSTUS\tCDS\t1640990\t1643609\t1\t-\t0\ttranscript_id \"g21651.t1\"; gene_id \"g21651\";\r\n", "1\t1665090\t1665092\t1\tAUGUSTUS\tCDS\t1664341\t1665225\t1\t+\t0\ttranscript_id \"g21652.t1\"; gene_id \"g21652\";\r\n", "1\t1665156\t1665158\t1\tAUGUSTUS\tCDS\t1664341\t1665225\t1\t+\t0\ttranscript_id \"g21652.t1\"; gene_id \"g21652\";\r\n", "1\t1665164\t1665166\t1\tAUGUSTUS\tCDS\t1664341\t1665225\t1\t+\t0\ttranscript_id \"g21652.t1\"; gene_id \"g21652\";\r\n", "\r\n", "==> Meth11_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-sparseMeth.bed-mcCDS <==\r\n", "1\t581543\t581545\t1\tAUGUSTUS\tCDS\t581411\t581815\t0.67\t-\t0\ttranscript_id \"g21577.t1\"; gene_id \"g21577\";\r\n", "1\t581570\t581572\t1\tAUGUSTUS\tCDS\t581411\t581815\t0.67\t-\t0\ttranscript_id \"g21577.t1\"; gene_id \"g21577\";\r\n", "1\t744050\t744052\t1\tAUGUSTUS\tCDS\t743708\t745054\t0.98\t-\t0\ttranscript_id \"g21595.t1\"; gene_id \"g21595\";\r\n", "1\t744608\t744610\t1\tAUGUSTUS\tCDS\t743708\t745054\t0.98\t-\t0\ttranscript_id \"g21595.t1\"; gene_id \"g21595\";\r\n", "1\t785550\t785552\t1\tAUGUSTUS\tCDS\t785545\t785798\t0.84\t-\t0\ttranscript_id \"g21597.t1\"; gene_id \"g21597\";\r\n", "1\t786094\t786096\t1\tAUGUSTUS\tCDS\t785899\t786207\t0.98\t-\t0\ttranscript_id \"g21598.t1\"; gene_id \"g21598\";\r\n", "1\t1236857\t1236859\t1\tAUGUSTUS\tCDS\t1234405\t1236984\t1\t-\t0\ttranscript_id \"g21628.t1\"; gene_id \"g21628\";\r\n", "1\t1236887\t1236889\t1\tAUGUSTUS\tCDS\t1234405\t1236984\t1\t-\t0\ttranscript_id \"g21628.t1\"; gene_id \"g21628\";\r\n", "1\t1236894\t1236896\t1\tAUGUSTUS\tCDS\t1234405\t1236984\t1\t-\t0\ttranscript_id \"g21628.t1\"; gene_id \"g21628\";\r\n", "1\t1427032\t1427034\t1\tAUGUSTUS\tCDS\t1427003\t1427857\t1\t-\t0\ttranscript_id \"g21637.t1\"; gene_id \"g21637\";\r\n", "\r\n", "==> Meth11_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-unMeth.bed-mcCDS <==\r\n", "1\t238620\t238622\t1\tAUGUSTUS\tCDS\t237955\t238956\t1\t+\t0\ttranscript_id \"g21550.t1\"; gene_id \"g21550\";\r\n", "1\t362250\t362252\t1\tAUGUSTUS\tCDS\t361628\t363571\t0.97\t-\t0\ttranscript_id \"g21558.t1\"; gene_id \"g21558\";\r\n", "1\t362276\t362278\t1\tAUGUSTUS\tCDS\t361628\t363571\t0.97\t-\t0\ttranscript_id \"g21558.t1\"; gene_id \"g21558\";\r\n", "1\t362309\t362311\t1\tAUGUSTUS\tCDS\t361628\t363571\t0.97\t-\t0\ttranscript_id \"g21558.t1\"; gene_id \"g21558\";\r\n", "1\t362320\t362322\t1\tAUGUSTUS\tCDS\t361628\t363571\t0.97\t-\t0\ttranscript_id \"g21558.t1\"; gene_id \"g21558\";\r\n", "1\t362324\t362326\t1\tAUGUSTUS\tCDS\t361628\t363571\t0.97\t-\t0\ttranscript_id \"g21558.t1\"; gene_id \"g21558\";\r\n", "1\t362349\t362351\t1\tAUGUSTUS\tCDS\t361628\t363571\t0.97\t-\t0\ttranscript_id \"g21558.t1\"; gene_id \"g21558\";\r\n", "1\t362361\t362363\t1\tAUGUSTUS\tCDS\t361628\t363571\t0.97\t-\t0\ttranscript_id \"g21558.t1\"; gene_id \"g21558\";\r\n", "1\t362367\t362369\t1\tAUGUSTUS\tCDS\t361628\t363571\t0.97\t-\t0\ttranscript_id \"g21558.t1\"; gene_id \"g21558\";\r\n", "1\t362406\t362408\t1\tAUGUSTUS\tCDS\t361628\t363571\t0.97\t-\t0\ttranscript_id \"g21558.t1\"; gene_id \"g21558\";\r\n", "\r\n", "==> Meth11_R1_001_val_1_bismark_bt2_pe._10x.bedgraph.bed-mcCDS <==\r\n", "1\t238620\t238622\t1\tAUGUSTUS\tCDS\t237955\t238956\t1\t+\t0\ttranscript_id \"g21550.t1\"; gene_id \"g21550\";\r\n", "1\t362250\t362252\t1\tAUGUSTUS\tCDS\t361628\t363571\t0.97\t-\t0\ttranscript_id \"g21558.t1\"; gene_id \"g21558\";\r\n", "1\t362276\t362278\t1\tAUGUSTUS\tCDS\t361628\t363571\t0.97\t-\t0\ttranscript_id \"g21558.t1\"; gene_id \"g21558\";\r\n", "1\t362309\t362311\t1\tAUGUSTUS\tCDS\t361628\t363571\t0.97\t-\t0\ttranscript_id \"g21558.t1\"; gene_id \"g21558\";\r\n", "1\t362320\t362322\t1\tAUGUSTUS\tCDS\t361628\t363571\t0.97\t-\t0\ttranscript_id \"g21558.t1\"; gene_id \"g21558\";\r\n", "1\t362324\t362326\t1\tAUGUSTUS\tCDS\t361628\t363571\t0.97\t-\t0\ttranscript_id \"g21558.t1\"; gene_id \"g21558\";\r\n", "1\t362349\t362351\t1\tAUGUSTUS\tCDS\t361628\t363571\t0.97\t-\t0\ttranscript_id \"g21558.t1\"; gene_id \"g21558\";\r\n", "1\t362361\t362363\t1\tAUGUSTUS\tCDS\t361628\t363571\t0.97\t-\t0\ttranscript_id \"g21558.t1\"; gene_id \"g21558\";\r\n", "1\t362367\t362369\t1\tAUGUSTUS\tCDS\t361628\t363571\t0.97\t-\t0\ttranscript_id \"g21558.t1\"; gene_id \"g21558\";\r\n", "1\t362406\t362408\t1\tAUGUSTUS\tCDS\t361628\t363571\t0.97\t-\t0\ttranscript_id \"g21558.t1\"; gene_id \"g21558\";\r\n", "\r\n", "==> Meth12_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-Meth.bed-mcCDS <==\r\n", "1\t789388\t789390\t1\tAUGUSTUS\tCDS\t789380\t789726\t0.68\t-\t2\ttranscript_id \"g21600.t1\"; gene_id \"g21600\";\r\n", "1\t1264019\t1264021\t1\tAUGUSTUS\tCDS\t1262915\t1264300\t1\t-\t0\ttranscript_id \"g21628.t1\"; gene_id \"g21628\";\r\n", "1\t1264052\t1264054\t1\tAUGUSTUS\tCDS\t1262915\t1264300\t1\t-\t0\ttranscript_id \"g21628.t1\"; gene_id \"g21628\";\r\n", "1\t1264159\t1264161\t1\tAUGUSTUS\tCDS\t1262915\t1264300\t1\t-\t0\ttranscript_id \"g21628.t1\"; gene_id \"g21628\";\r\n", "1\t1264199\t1264201\t1\tAUGUSTUS\tCDS\t1262915\t1264300\t1\t-\t0\ttranscript_id \"g21628.t1\"; gene_id \"g21628\";\r\n", "1\t1270851\t1270853\t1\tAUGUSTUS\tCDS\t1270851\t1270989\t1\t-\t0\ttranscript_id \"g21628.t1\"; gene_id \"g21628\";\r\n", "1\t1270897\t1270899\t1\tAUGUSTUS\tCDS\t1270851\t1270989\t1\t-\t0\ttranscript_id \"g21628.t1\"; gene_id \"g21628\";\r\n", "1\t1270933\t1270935\t1\tAUGUSTUS\tCDS\t1270851\t1270989\t1\t-\t0\ttranscript_id \"g21628.t1\"; gene_id \"g21628\";\r\n", "1\t1270937\t1270939\t1\tAUGUSTUS\tCDS\t1270851\t1270989\t1\t-\t0\ttranscript_id \"g21628.t1\"; gene_id \"g21628\";\r\n", "1\t1373791\t1373793\t1\tAUGUSTUS\tCDS\t1373782\t1373975\t1\t-\t0\ttranscript_id \"g21633.t1\"; gene_id \"g21633\";\r\n", "\r\n", "==> Meth12_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-sparseMeth.bed-mcCDS <==\r\n", "1\t420896\t420898\t1\tAUGUSTUS\tCDS\t420478\t420918\t0.52\t+\t0\ttranscript_id \"g21562.t1\"; gene_id \"g21562\";\r\n", "1\t744671\t744673\t1\tAUGUSTUS\tCDS\t743708\t745054\t0.98\t-\t0\ttranscript_id \"g21595.t1\"; gene_id \"g21595\";\r\n", "1\t789590\t789592\t1\tAUGUSTUS\tCDS\t789380\t789726\t0.68\t-\t2\ttranscript_id \"g21600.t1\"; gene_id \"g21600\";\r\n", "1\t789598\t789600\t1\tAUGUSTUS\tCDS\t789380\t789726\t0.68\t-\t2\ttranscript_id \"g21600.t1\"; gene_id \"g21600\";\r\n", "1\t789613\t789615\t1\tAUGUSTUS\tCDS\t789380\t789726\t0.68\t-\t2\ttranscript_id \"g21600.t1\"; gene_id \"g21600\";\r\n", "1\t789648\t789650\t1\tAUGUSTUS\tCDS\t789380\t789726\t0.68\t-\t2\ttranscript_id \"g21600.t1\"; gene_id \"g21600\";\r\n", "1\t789673\t789675\t1\tAUGUSTUS\tCDS\t789380\t789726\t0.68\t-\t2\ttranscript_id \"g21600.t1\"; gene_id \"g21600\";\r\n", "1\t789690\t789692\t1\tAUGUSTUS\tCDS\t789380\t789726\t0.68\t-\t2\ttranscript_id \"g21600.t1\"; gene_id \"g21600\";\r\n", "1\t789693\t789695\t1\tAUGUSTUS\tCDS\t789380\t789726\t0.68\t-\t2\ttranscript_id \"g21600.t1\"; gene_id \"g21600\";\r\n", "1\t789708\t789710\t1\tAUGUSTUS\tCDS\t789380\t789726\t0.68\t-\t2\ttranscript_id \"g21600.t1\"; gene_id \"g21600\";\r\n", "\r\n", "==> Meth12_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-unMeth.bed-mcCDS <==\r\n", "1\t218054\t218056\t1\tAUGUSTUS\tCDS\t218011\t218415\t0.95\t-\t0\ttranscript_id \"g21549.t1\"; gene_id \"g21549\";\r\n", "1\t218208\t218210\t1\tAUGUSTUS\tCDS\t218011\t218415\t0.95\t-\t0\ttranscript_id \"g21549.t1\"; gene_id \"g21549\";\r\n", "1\t218217\t218219\t1\tAUGUSTUS\tCDS\t218011\t218415\t0.95\t-\t0\ttranscript_id \"g21549.t1\"; gene_id \"g21549\";\r\n", "1\t218240\t218242\t1\tAUGUSTUS\tCDS\t218011\t218415\t0.95\t-\t0\ttranscript_id \"g21549.t1\"; gene_id \"g21549\";\r\n", "1\t218283\t218285\t1\tAUGUSTUS\tCDS\t218011\t218415\t0.95\t-\t0\ttranscript_id \"g21549.t1\"; gene_id \"g21549\";\r\n", "1\t218298\t218300\t1\tAUGUSTUS\tCDS\t218011\t218415\t0.95\t-\t0\ttranscript_id \"g21549.t1\"; gene_id \"g21549\";\r\n", "1\t218312\t218314\t1\tAUGUSTUS\tCDS\t218011\t218415\t0.95\t-\t0\ttranscript_id \"g21549.t1\"; gene_id \"g21549\";\r\n", "1\t218320\t218322\t1\tAUGUSTUS\tCDS\t218011\t218415\t0.95\t-\t0\ttranscript_id \"g21549.t1\"; gene_id \"g21549\";\r\n", "1\t332309\t332311\t1\tAUGUSTUS\tCDS\t332282\t332497\t1\t-\t0\ttranscript_id \"g21555.t1\"; gene_id \"g21555\";\r\n", "1\t332373\t332375\t1\tAUGUSTUS\tCDS\t332282\t332497\t1\t-\t0\ttranscript_id \"g21555.t1\"; gene_id \"g21555\";\r\n", "\r\n", "==> Meth12_R1_001_val_1_bismark_bt2_pe._10x.bedgraph.bed-mcCDS <==\r\n", "1\t218054\t218056\t1\tAUGUSTUS\tCDS\t218011\t218415\t0.95\t-\t0\ttranscript_id \"g21549.t1\"; gene_id \"g21549\";\r\n", "1\t218208\t218210\t1\tAUGUSTUS\tCDS\t218011\t218415\t0.95\t-\t0\ttranscript_id \"g21549.t1\"; gene_id \"g21549\";\r\n", "1\t218217\t218219\t1\tAUGUSTUS\tCDS\t218011\t218415\t0.95\t-\t0\ttranscript_id \"g21549.t1\"; gene_id \"g21549\";\r\n", "1\t218240\t218242\t1\tAUGUSTUS\tCDS\t218011\t218415\t0.95\t-\t0\ttranscript_id \"g21549.t1\"; gene_id \"g21549\";\r\n", "1\t218283\t218285\t1\tAUGUSTUS\tCDS\t218011\t218415\t0.95\t-\t0\ttranscript_id \"g21549.t1\"; gene_id \"g21549\";\r\n", "1\t218298\t218300\t1\tAUGUSTUS\tCDS\t218011\t218415\t0.95\t-\t0\ttranscript_id \"g21549.t1\"; gene_id \"g21549\";\r\n", "1\t218312\t218314\t1\tAUGUSTUS\tCDS\t218011\t218415\t0.95\t-\t0\ttranscript_id \"g21549.t1\"; gene_id \"g21549\";\r\n", "1\t218320\t218322\t1\tAUGUSTUS\tCDS\t218011\t218415\t0.95\t-\t0\ttranscript_id \"g21549.t1\"; gene_id \"g21549\";\r\n", "1\t332309\t332311\t1\tAUGUSTUS\tCDS\t332282\t332497\t1\t-\t0\ttranscript_id \"g21555.t1\"; gene_id \"g21555\";\r\n", "1\t332373\t332375\t1\tAUGUSTUS\tCDS\t332282\t332497\t1\t-\t0\ttranscript_id \"g21555.t1\"; gene_id \"g21555\";\r\n", "\r\n", "==> Meth13_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-Meth.bed-mcCDS <==\r\n", "1\t58618\t58620\t1\tAUGUSTUS\tCDS\t58322\t59506\t1\t-\t0\ttranscript_id \"g21535.t1\"; gene_id \"g21535\";\r\n", "1\t58745\t58747\t1\tAUGUSTUS\tCDS\t58322\t59506\t1\t-\t0\ttranscript_id \"g21535.t1\"; gene_id \"g21535\";\r\n", "1\t58764\t58766\t1\tAUGUSTUS\tCDS\t58322\t59506\t1\t-\t0\ttranscript_id \"g21535.t1\"; gene_id \"g21535\";\r\n", "1\t58792\t58794\t1\tAUGUSTUS\tCDS\t58322\t59506\t1\t-\t0\ttranscript_id \"g21535.t1\"; gene_id \"g21535\";\r\n", "1\t1367668\t1367670\t1\tAUGUSTUS\tCDS\t1367658\t1367706\t1\t-\t0\ttranscript_id \"g21633.t1\"; gene_id \"g21633\";\r\n", "1\t1641547\t1641549\t1\tAUGUSTUS\tCDS\t1640990\t1643609\t1\t-\t0\ttranscript_id \"g21651.t1\"; gene_id \"g21651\";\r\n", "1\t1641670\t1641672\t1\tAUGUSTUS\tCDS\t1640990\t1643609\t1\t-\t0\ttranscript_id \"g21651.t1\"; gene_id \"g21651\";\r\n", "1\t1641723\t1641725\t1\tAUGUSTUS\tCDS\t1640990\t1643609\t1\t-\t0\ttranscript_id \"g21651.t1\"; gene_id \"g21651\";\r\n", "1\t1677775\t1677777\t1\tAUGUSTUS\tCDS\t1677752\t1677857\t1\t+\t0\ttranscript_id \"g21653.t1\"; gene_id \"g21653\";\r\n", "1\t1750014\t1750016\t1\tAUGUSTUS\tCDS\t1749946\t1750092\t1\t-\t0\ttranscript_id \"g21659.t1\"; gene_id \"g21659\";\r\n", "\r\n", "==> Meth13_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-sparseMeth.bed-mcCDS <==\r\n", "1\t45163\t45165\t1\tAUGUSTUS\tCDS\t45038\t45208\t1\t+\t2\ttranscript_id \"g21534.t1\"; gene_id \"g21534\";\r\n", "1\t526047\t526049\t1\tAUGUSTUS\tCDS\t524298\t526199\t1\t-\t0\ttranscript_id \"g21573.t1\"; gene_id \"g21573\";\r\n", "1\t607861\t607863\t1\tAUGUSTUS\tCDS\t607804\t608337\t1\t+\t0\ttranscript_id \"g21581.t1\"; gene_id \"g21581\";\r\n", "1\t894945\t894947\t1\tAUGUSTUS\tCDS\t894806\t894956\t0.52\t+\t1\ttranscript_id \"g21603.t1\"; gene_id \"g21603\";\r\n", "1\t940040\t940042\t1\tAUGUSTUS\tCDS\t938963\t941032\t0.99\t-\t0\ttranscript_id \"g21607.t1\"; gene_id \"g21607\";\r\n", "1\t960189\t960191\t1\tAUGUSTUS\tCDS\t960052\t960222\t1\t-\t2\ttranscript_id \"g21609.t1\"; gene_id \"g21609\";\r\n", "1\t1130680\t1130682\t1\tAUGUSTUS\tCDS\t1130441\t1131316\t0.76\t+\t1\ttranscript_id \"g21620.t1\"; gene_id \"g21620\";\r\n", "1\t1587400\t1587402\t1\tAUGUSTUS\tCDS\t1587359\t1587473\t1\t+\t1\ttranscript_id \"g21645.t1\"; gene_id \"g21645\";\r\n", "1\t1677795\t1677797\t1\tAUGUSTUS\tCDS\t1677752\t1677857\t1\t+\t0\ttranscript_id \"g21653.t1\"; gene_id \"g21653\";\r\n", "1\t1677798\t1677800\t1\tAUGUSTUS\tCDS\t1677752\t1677857\t1\t+\t0\ttranscript_id \"g21653.t1\"; gene_id \"g21653\";\r\n", "\r\n", "==> Meth13_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-unMeth.bed-mcCDS <==\r\n", "1\t22445\t22447\t1\tAUGUSTUS\tCDS\t22321\t22608\t0.55\t-\t0\ttranscript_id \"g21533.t1\"; gene_id \"g21533\";\r\n", "1\t22505\t22507\t1\tAUGUSTUS\tCDS\t22321\t22608\t0.55\t-\t0\ttranscript_id \"g21533.t1\"; gene_id \"g21533\";\r\n", "1\t22513\t22515\t1\tAUGUSTUS\tCDS\t22321\t22608\t0.55\t-\t0\ttranscript_id \"g21533.t1\"; gene_id \"g21533\";\r\n", "1\t22531\t22533\t1\tAUGUSTUS\tCDS\t22321\t22608\t0.55\t-\t0\ttranscript_id \"g21533.t1\"; gene_id \"g21533\";\r\n", "1\t22534\t22536\t1\tAUGUSTUS\tCDS\t22321\t22608\t0.55\t-\t0\ttranscript_id \"g21533.t1\"; gene_id \"g21533\";\r\n", "1\t22547\t22549\t1\tAUGUSTUS\tCDS\t22321\t22608\t0.55\t-\t0\ttranscript_id \"g21533.t1\"; gene_id \"g21533\";\r\n", "1\t22563\t22565\t1\tAUGUSTUS\tCDS\t22321\t22608\t0.55\t-\t0\ttranscript_id \"g21533.t1\"; gene_id \"g21533\";\r\n", "1\t45046\t45048\t1\tAUGUSTUS\tCDS\t45038\t45208\t1\t+\t2\ttranscript_id \"g21534.t1\"; gene_id \"g21534\";\r\n", "1\t45070\t45072\t1\tAUGUSTUS\tCDS\t45038\t45208\t1\t+\t2\ttranscript_id \"g21534.t1\"; gene_id \"g21534\";\r\n", "1\t45110\t45112\t1\tAUGUSTUS\tCDS\t45038\t45208\t1\t+\t2\ttranscript_id \"g21534.t1\"; gene_id \"g21534\";\r\n", "\r\n", "==> Meth13_R1_001_val_1_bismark_bt2_pe._10x.bedgraph.bed-mcCDS <==\r\n", "1\t22445\t22447\t1\tAUGUSTUS\tCDS\t22321\t22608\t0.55\t-\t0\ttranscript_id \"g21533.t1\"; gene_id \"g21533\";\r\n", "1\t22505\t22507\t1\tAUGUSTUS\tCDS\t22321\t22608\t0.55\t-\t0\ttranscript_id \"g21533.t1\"; gene_id \"g21533\";\r\n", "1\t22513\t22515\t1\tAUGUSTUS\tCDS\t22321\t22608\t0.55\t-\t0\ttranscript_id \"g21533.t1\"; gene_id \"g21533\";\r\n", "1\t22531\t22533\t1\tAUGUSTUS\tCDS\t22321\t22608\t0.55\t-\t0\ttranscript_id \"g21533.t1\"; gene_id \"g21533\";\r\n", "1\t22534\t22536\t1\tAUGUSTUS\tCDS\t22321\t22608\t0.55\t-\t0\ttranscript_id \"g21533.t1\"; gene_id \"g21533\";\r\n", "1\t22547\t22549\t1\tAUGUSTUS\tCDS\t22321\t22608\t0.55\t-\t0\ttranscript_id \"g21533.t1\"; gene_id \"g21533\";\r\n", "1\t22563\t22565\t1\tAUGUSTUS\tCDS\t22321\t22608\t0.55\t-\t0\ttranscript_id \"g21533.t1\"; gene_id \"g21533\";\r\n", "1\t45046\t45048\t1\tAUGUSTUS\tCDS\t45038\t45208\t1\t+\t2\ttranscript_id \"g21534.t1\"; gene_id \"g21534\";\r\n", "1\t45070\t45072\t1\tAUGUSTUS\tCDS\t45038\t45208\t1\t+\t2\ttranscript_id \"g21534.t1\"; gene_id \"g21534\";\r\n", "1\t45110\t45112\t1\tAUGUSTUS\tCDS\t45038\t45208\t1\t+\t2\ttranscript_id \"g21534.t1\"; gene_id \"g21534\";\r\n", "\r\n", "==> Meth14_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-Meth.bed-mcCDS <==\r\n", "1\t58618\t58620\t1\tAUGUSTUS\tCDS\t58322\t59506\t1\t-\t0\ttranscript_id \"g21535.t1\"; gene_id \"g21535\";\r\n", "1\t58745\t58747\t1\tAUGUSTUS\tCDS\t58322\t59506\t1\t-\t0\ttranscript_id \"g21535.t1\"; gene_id \"g21535\";\r\n", "1\t58764\t58766\t1\tAUGUSTUS\tCDS\t58322\t59506\t1\t-\t0\ttranscript_id \"g21535.t1\"; gene_id \"g21535\";\r\n", "1\t58792\t58794\t1\tAUGUSTUS\tCDS\t58322\t59506\t1\t-\t0\ttranscript_id \"g21535.t1\"; gene_id \"g21535\";\r\n", "1\t1367668\t1367670\t1\tAUGUSTUS\tCDS\t1367658\t1367706\t1\t-\t0\ttranscript_id \"g21633.t1\"; gene_id \"g21633\";\r\n", "1\t1750088\t1750090\t1\tAUGUSTUS\tCDS\t1749946\t1750092\t1\t-\t0\ttranscript_id \"g21659.t1\"; gene_id \"g21659\";\r\n", "1\t1869676\t1869678\t1\tAUGUSTUS\tCDS\t1869579\t1869678\t1\t+\t2\ttranscript_id \"g21672.t1\"; gene_id \"g21672\";\r\n", "1\t3062918\t3062920\t1\tAUGUSTUS\tCDS\t3062915\t3063160\t1\t-\t0\ttranscript_id \"g21750.t1\"; gene_id \"g21750\";\r\n", "1\t3062991\t3062993\t1\tAUGUSTUS\tCDS\t3062915\t3063160\t1\t-\t0\ttranscript_id \"g21750.t1\"; gene_id \"g21750\";\r\n", "1\t3063000\t3063002\t1\tAUGUSTUS\tCDS\t3062915\t3063160\t1\t-\t0\ttranscript_id \"g21750.t1\"; gene_id \"g21750\";\r\n", "\r\n", "==> Meth14_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-sparseMeth.bed-mcCDS <==\r\n", "1\t587749\t587751\t1\tAUGUSTUS\tCDS\t587602\t587776\t0.7\t-\t0\ttranscript_id \"g21579.t1\"; gene_id \"g21579\";\r\n", "1\t743735\t743737\t1\tAUGUSTUS\tCDS\t743708\t745054\t0.98\t-\t0\ttranscript_id \"g21595.t1\"; gene_id \"g21595\";\r\n", "1\t743825\t743827\t1\tAUGUSTUS\tCDS\t743708\t745054\t0.98\t-\t0\ttranscript_id \"g21595.t1\"; gene_id \"g21595\";\r\n", "1\t744333\t744335\t1\tAUGUSTUS\tCDS\t743708\t745054\t0.98\t-\t0\ttranscript_id \"g21595.t1\"; gene_id \"g21595\";\r\n", "1\t744680\t744682\t1\tAUGUSTUS\tCDS\t743708\t745054\t0.98\t-\t0\ttranscript_id \"g21595.t1\"; gene_id \"g21595\";\r\n", "1\t785550\t785552\t1\tAUGUSTUS\tCDS\t785545\t785798\t0.84\t-\t0\ttranscript_id \"g21597.t1\"; gene_id \"g21597\";\r\n", "1\t785779\t785781\t1\tAUGUSTUS\tCDS\t785545\t785798\t0.84\t-\t0\ttranscript_id \"g21597.t1\"; gene_id \"g21597\";\r\n", "1\t961234\t961236\t1\tAUGUSTUS\tCDS\t961127\t961348\t1\t-\t2\ttranscript_id \"g21609.t1\"; gene_id \"g21609\";\r\n", "1\t1246976\t1246978\t1\tAUGUSTUS\tCDS\t1246948\t1247026\t1\t-\t0\ttranscript_id \"g21628.t1\"; gene_id \"g21628\";\r\n", "1\t1432471\t1432473\t1\tAUGUSTUS\tCDS\t1431855\t1432904\t1\t-\t0\ttranscript_id \"g21638.t1\"; gene_id \"g21638\";\r\n", "\r\n", "==> Meth14_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-unMeth.bed-mcCDS <==\r\n", "1\t45046\t45048\t1\tAUGUSTUS\tCDS\t45038\t45208\t1\t+\t2\ttranscript_id \"g21534.t1\"; gene_id \"g21534\";\r\n", "1\t45070\t45072\t1\tAUGUSTUS\tCDS\t45038\t45208\t1\t+\t2\ttranscript_id \"g21534.t1\"; gene_id \"g21534\";\r\n", "1\t45110\t45112\t1\tAUGUSTUS\tCDS\t45038\t45208\t1\t+\t2\ttranscript_id \"g21534.t1\"; gene_id \"g21534\";\r\n", "1\t45116\t45118\t1\tAUGUSTUS\tCDS\t45038\t45208\t1\t+\t2\ttranscript_id \"g21534.t1\"; gene_id \"g21534\";\r\n", "1\t45128\t45130\t1\tAUGUSTUS\tCDS\t45038\t45208\t1\t+\t2\ttranscript_id \"g21534.t1\"; gene_id \"g21534\";\r\n", "1\t45154\t45156\t1\tAUGUSTUS\tCDS\t45038\t45208\t1\t+\t2\ttranscript_id \"g21534.t1\"; gene_id \"g21534\";\r\n", "1\t349163\t349165\t1\tAUGUSTUS\tCDS\t349160\t349261\t1\t+\t0\ttranscript_id \"g21556.t1\"; gene_id \"g21556\";\r\n", "1\t349182\t349184\t1\tAUGUSTUS\tCDS\t349160\t349261\t1\t+\t0\ttranscript_id \"g21556.t1\"; gene_id \"g21556\";\r\n", "1\t349188\t349190\t1\tAUGUSTUS\tCDS\t349160\t349261\t1\t+\t0\ttranscript_id \"g21556.t1\"; gene_id \"g21556\";\r\n", "1\t349242\t349244\t1\tAUGUSTUS\tCDS\t349160\t349261\t1\t+\t0\ttranscript_id \"g21556.t1\"; gene_id \"g21556\";\r\n", "\r\n", "==> Meth14_R1_001_val_1_bismark_bt2_pe._10x.bedgraph.bed-mcCDS <==\r\n", "1\t45046\t45048\t1\tAUGUSTUS\tCDS\t45038\t45208\t1\t+\t2\ttranscript_id \"g21534.t1\"; gene_id \"g21534\";\r\n", "1\t45070\t45072\t1\tAUGUSTUS\tCDS\t45038\t45208\t1\t+\t2\ttranscript_id \"g21534.t1\"; gene_id \"g21534\";\r\n", "1\t45110\t45112\t1\tAUGUSTUS\tCDS\t45038\t45208\t1\t+\t2\ttranscript_id \"g21534.t1\"; gene_id \"g21534\";\r\n", "1\t45116\t45118\t1\tAUGUSTUS\tCDS\t45038\t45208\t1\t+\t2\ttranscript_id \"g21534.t1\"; gene_id \"g21534\";\r\n", "1\t45128\t45130\t1\tAUGUSTUS\tCDS\t45038\t45208\t1\t+\t2\ttranscript_id \"g21534.t1\"; gene_id \"g21534\";\r\n", "1\t45154\t45156\t1\tAUGUSTUS\tCDS\t45038\t45208\t1\t+\t2\ttranscript_id \"g21534.t1\"; gene_id \"g21534\";\r\n", "1\t58618\t58620\t1\tAUGUSTUS\tCDS\t58322\t59506\t1\t-\t0\ttranscript_id \"g21535.t1\"; gene_id \"g21535\";\r\n", "1\t58745\t58747\t1\tAUGUSTUS\tCDS\t58322\t59506\t1\t-\t0\ttranscript_id \"g21535.t1\"; gene_id \"g21535\";\r\n", "1\t58764\t58766\t1\tAUGUSTUS\tCDS\t58322\t59506\t1\t-\t0\ttranscript_id \"g21535.t1\"; gene_id \"g21535\";\r\n", "1\t58792\t58794\t1\tAUGUSTUS\tCDS\t58322\t59506\t1\t-\t0\ttranscript_id \"g21535.t1\"; gene_id \"g21535\";\r\n", "\r\n", "==> Meth15_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-Meth.bed-mcCDS <==\r\n", "1\t58618\t58620\t1\tAUGUSTUS\tCDS\t58322\t59506\t1\t-\t0\ttranscript_id \"g21535.t1\"; gene_id \"g21535\";\r\n", "1\t58745\t58747\t1\tAUGUSTUS\tCDS\t58322\t59506\t1\t-\t0\ttranscript_id \"g21535.t1\"; gene_id \"g21535\";\r\n", "1\t58764\t58766\t1\tAUGUSTUS\tCDS\t58322\t59506\t1\t-\t0\ttranscript_id \"g21535.t1\"; gene_id \"g21535\";\r\n", "1\t58792\t58794\t1\tAUGUSTUS\tCDS\t58322\t59506\t1\t-\t0\ttranscript_id \"g21535.t1\"; gene_id \"g21535\";\r\n", "1\t1641547\t1641549\t1\tAUGUSTUS\tCDS\t1640990\t1643609\t1\t-\t0\ttranscript_id \"g21651.t1\"; gene_id \"g21651\";\r\n", "1\t1641670\t1641672\t1\tAUGUSTUS\tCDS\t1640990\t1643609\t1\t-\t0\ttranscript_id \"g21651.t1\"; gene_id \"g21651\";\r\n", "1\t1641723\t1641725\t1\tAUGUSTUS\tCDS\t1640990\t1643609\t1\t-\t0\ttranscript_id \"g21651.t1\"; gene_id \"g21651\";\r\n", "1\t1750088\t1750090\t1\tAUGUSTUS\tCDS\t1749946\t1750092\t1\t-\t0\ttranscript_id \"g21659.t1\"; gene_id \"g21659\";\r\n", "1\t1751639\t1751641\t1\tAUGUSTUS\tCDS\t1751042\t1751722\t1\t-\t0\ttranscript_id \"g21659.t1\"; gene_id \"g21659\";\r\n", "1\t1829006\t1829008\t1\tAUGUSTUS\tCDS\t1828992\t1829109\t1\t+\t0\ttranscript_id \"g21667.t1\"; gene_id \"g21667\";\r\n", "\r\n", "==> Meth15_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-sparseMeth.bed-mcCDS <==\r\n", "1\t587667\t587669\t1\tAUGUSTUS\tCDS\t587602\t587776\t0.7\t-\t0\ttranscript_id \"g21579.t1\"; gene_id \"g21579\";\r\n", "1\t946097\t946099\t1\tAUGUSTUS\tCDS\t945184\t946113\t0.98\t+\t0\ttranscript_id \"g21608.t1\"; gene_id \"g21608\";\r\n", "1\t1064399\t1064401\t1\tAUGUSTUS\tCDS\t1064077\t1065057\t1\t+\t0\ttranscript_id \"g21615.t1\"; gene_id \"g21615\";\r\n", "1\t1134015\t1134017\t1\tAUGUSTUS\tCDS\t1133593\t1134134\t0.98\t+\t2\ttranscript_id \"g21620.t1\"; gene_id \"g21620\";\r\n", "1\t1174115\t1174117\t1\tAUGUSTUS\tCDS\t1173914\t1174302\t0.48\t-\t1\ttranscript_id \"g21623.t1\"; gene_id \"g21623\";\r\n", "1\t1677775\t1677777\t1\tAUGUSTUS\tCDS\t1677752\t1677857\t1\t+\t0\ttranscript_id \"g21653.t1\"; gene_id \"g21653\";\r\n", "1\t1924686\t1924688\t1\tAUGUSTUS\tCDS\t1924608\t1926509\t0.89\t-\t0\ttranscript_id \"g21678.t1\"; gene_id \"g21678\";\r\n", "1\t1953558\t1953560\t1\tAUGUSTUS\tCDS\t1953481\t1953613\t1\t+\t0\ttranscript_id \"g21683.t1\"; gene_id \"g21683\";\r\n", "1\t2209954\t2209956\t1\tAUGUSTUS\tCDS\t2209757\t2213174\t1\t-\t1\ttranscript_id \"g21700.t1\"; gene_id \"g21700\";\r\n", "1\t2211088\t2211090\t1\tAUGUSTUS\tCDS\t2209757\t2213174\t1\t-\t1\ttranscript_id \"g21700.t1\"; gene_id \"g21700\";\r\n", "\r\n", "==> Meth15_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-unMeth.bed-mcCDS <==\r\n", "1\t148380\t148382\t1\tAUGUSTUS\tCDS\t148344\t148524\t0.46\t+\t0\ttranscript_id \"g21541.t1\"; gene_id \"g21541\";\r\n", "1\t148390\t148392\t1\tAUGUSTUS\tCDS\t148344\t148524\t0.46\t+\t0\ttranscript_id \"g21541.t1\"; gene_id \"g21541\";\r\n", "1\t148392\t148394\t1\tAUGUSTUS\tCDS\t148344\t148524\t0.46\t+\t0\ttranscript_id \"g21541.t1\"; gene_id \"g21541\";\r\n", "1\t148396\t148398\t1\tAUGUSTUS\tCDS\t148344\t148524\t0.46\t+\t0\ttranscript_id \"g21541.t1\"; gene_id \"g21541\";\r\n", "1\t148406\t148408\t1\tAUGUSTUS\tCDS\t148344\t148524\t0.46\t+\t0\ttranscript_id \"g21541.t1\"; gene_id \"g21541\";\r\n", "1\t148429\t148431\t1\tAUGUSTUS\tCDS\t148344\t148524\t0.46\t+\t0\ttranscript_id \"g21541.t1\"; gene_id \"g21541\";\r\n", "1\t148451\t148453\t1\tAUGUSTUS\tCDS\t148344\t148524\t0.46\t+\t0\ttranscript_id \"g21541.t1\"; gene_id \"g21541\";\r\n", "1\t148455\t148457\t1\tAUGUSTUS\tCDS\t148344\t148524\t0.46\t+\t0\ttranscript_id \"g21541.t1\"; gene_id \"g21541\";\r\n", "1\t148457\t148459\t1\tAUGUSTUS\tCDS\t148344\t148524\t0.46\t+\t0\ttranscript_id \"g21541.t1\"; gene_id \"g21541\";\r\n", "1\t148462\t148464\t1\tAUGUSTUS\tCDS\t148344\t148524\t0.46\t+\t0\ttranscript_id \"g21541.t1\"; gene_id \"g21541\";\r\n", "\r\n", "==> Meth15_R1_001_val_1_bismark_bt2_pe._10x.bedgraph.bed-mcCDS <==\r\n", "1\t58618\t58620\t1\tAUGUSTUS\tCDS\t58322\t59506\t1\t-\t0\ttranscript_id \"g21535.t1\"; gene_id \"g21535\";\r\n", "1\t58745\t58747\t1\tAUGUSTUS\tCDS\t58322\t59506\t1\t-\t0\ttranscript_id \"g21535.t1\"; gene_id \"g21535\";\r\n", "1\t58764\t58766\t1\tAUGUSTUS\tCDS\t58322\t59506\t1\t-\t0\ttranscript_id \"g21535.t1\"; gene_id \"g21535\";\r\n", "1\t58792\t58794\t1\tAUGUSTUS\tCDS\t58322\t59506\t1\t-\t0\ttranscript_id \"g21535.t1\"; gene_id \"g21535\";\r\n", "1\t148380\t148382\t1\tAUGUSTUS\tCDS\t148344\t148524\t0.46\t+\t0\ttranscript_id \"g21541.t1\"; gene_id \"g21541\";\r\n", "1\t148390\t148392\t1\tAUGUSTUS\tCDS\t148344\t148524\t0.46\t+\t0\ttranscript_id \"g21541.t1\"; gene_id \"g21541\";\r\n", "1\t148392\t148394\t1\tAUGUSTUS\tCDS\t148344\t148524\t0.46\t+\t0\ttranscript_id \"g21541.t1\"; gene_id \"g21541\";\r\n", "1\t148396\t148398\t1\tAUGUSTUS\tCDS\t148344\t148524\t0.46\t+\t0\ttranscript_id \"g21541.t1\"; gene_id \"g21541\";\r\n", "1\t148406\t148408\t1\tAUGUSTUS\tCDS\t148344\t148524\t0.46\t+\t0\ttranscript_id \"g21541.t1\"; gene_id \"g21541\";\r\n", "1\t148429\t148431\t1\tAUGUSTUS\tCDS\t148344\t148524\t0.46\t+\t0\ttranscript_id \"g21541.t1\"; gene_id \"g21541\";\r\n", "\r\n", "==> Meth16_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-Meth.bed-mcCDS <==\r\n", "2\t1984196\t1984198\t2\tAUGUSTUS\tCDS\t1983612\t1984280\t0.89\t-\t0\ttranscript_id \"g21974.t1\"; gene_id \"g21974\";\r\n", "2\t3036148\t3036150\t2\tAUGUSTUS\tCDS\t3036135\t3036719\t0.61\t+\t0\ttranscript_id \"g22168.t1\"; gene_id \"g22168\";\r\n", "2\t3036160\t3036162\t2\tAUGUSTUS\tCDS\t3036135\t3036719\t0.61\t+\t0\ttranscript_id \"g22168.t1\"; gene_id \"g22168\";\r\n", "2\t3036163\t3036165\t2\tAUGUSTUS\tCDS\t3036135\t3036719\t0.61\t+\t0\ttranscript_id \"g22168.t1\"; gene_id \"g22168\";\r\n", "2\t3036512\t3036514\t2\tAUGUSTUS\tCDS\t3036135\t3036719\t0.61\t+\t0\ttranscript_id \"g22168.t1\"; gene_id \"g22168\";\r\n", "2\t3036532\t3036534\t2\tAUGUSTUS\tCDS\t3036135\t3036719\t0.61\t+\t0\ttranscript_id \"g22168.t1\"; gene_id \"g22168\";\r\n", "2\t3036538\t3036540\t2\tAUGUSTUS\tCDS\t3036135\t3036719\t0.61\t+\t0\ttranscript_id \"g22168.t1\"; gene_id \"g22168\";\r\n", "2\t3308168\t3308170\t2\tAUGUSTUS\tCDS\t3308062\t3308430\t0.57\t-\t0\ttranscript_id \"g22219.t1\"; gene_id \"g22219\";\r\n", "6\t2130750\t2130752\t6\tAUGUSTUS\tCDS\t2130724\t2130850\t0.5\t-\t0\ttranscript_id \"g22813.t1\"; gene_id \"g22813\";\r\n", "6\t2130774\t2130776\t6\tAUGUSTUS\tCDS\t2130724\t2130850\t0.5\t-\t0\ttranscript_id \"g22813.t1\"; gene_id \"g22813\";\r\n", "\r\n", "==> Meth16_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-sparseMeth.bed-mcCDS <==\r\n", "2\t1704675\t1704677\t2\tAUGUSTUS\tCDS\t1704290\t1704742\t0.58\t-\t0\ttranscript_id \"g21949.t1\"; gene_id \"g21949\";\r\n", "2\t1704686\t1704688\t2\tAUGUSTUS\tCDS\t1704290\t1704742\t0.58\t-\t0\ttranscript_id \"g21949.t1\"; gene_id \"g21949\";\r\n", "2\t1704736\t1704738\t2\tAUGUSTUS\tCDS\t1704290\t1704742\t0.58\t-\t0\ttranscript_id \"g21949.t1\"; gene_id \"g21949\";\r\n", "2\t1984257\t1984259\t2\tAUGUSTUS\tCDS\t1983612\t1984280\t0.89\t-\t0\ttranscript_id \"g21974.t1\"; gene_id \"g21974\";\r\n", "7\t383493\t383495\t7\tAUGUSTUS\tCDS\t382188\t383802\t0.61\t+\t0\ttranscript_id \"g22900.t1\"; gene_id \"g22900\";\r\n", "9\t23860\t23862\t9\tAUGUSTUS\tCDS\t23704\t24276\t1\t+\t0\ttranscript_id \"g23074.t1\"; gene_id \"g23074\";\r\n", "9\t23869\t23871\t9\tAUGUSTUS\tCDS\t23704\t24276\t1\t+\t0\ttranscript_id \"g23074.t1\"; gene_id \"g23074\";\r\n", "9\t23873\t23875\t9\tAUGUSTUS\tCDS\t23704\t24276\t1\t+\t0\ttranscript_id \"g23074.t1\"; gene_id \"g23074\";\r\n", "9\t1537656\t1537658\t9\tAUGUSTUS\tCDS\t1537283\t1537756\t0.32\t-\t0\ttranscript_id \"g23195.t1\"; gene_id \"g23195\";\r\n", "10\t727460\t727462\t10\tAUGUSTUS\tCDS\t727432\t727737\t0.7\t+\t0\ttranscript_id \"g23341.t1\"; gene_id \"g23341\";\r\n", "\r\n", "==> Meth16_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-unMeth.bed-mcCDS <==\r\n", "2\t1984223\t1984225\t2\tAUGUSTUS\tCDS\t1983612\t1984280\t0.89\t-\t0\ttranscript_id \"g21974.t1\"; gene_id \"g21974\";\r\n", "4\t901529\t901531\t4\tAUGUSTUS\tCDS\t900901\t902022\t1\t+\t0\ttranscript_id \"g22337.t1\"; gene_id \"g22337\";\r\n", "4\t901536\t901538\t4\tAUGUSTUS\tCDS\t900901\t902022\t1\t+\t0\ttranscript_id \"g22337.t1\"; gene_id \"g22337\";\r\n", "4\t901541\t901543\t4\tAUGUSTUS\tCDS\t900901\t902022\t1\t+\t0\ttranscript_id \"g22337.t1\"; gene_id \"g22337\";\r\n", "5\t1653556\t1653558\t5\tAUGUSTUS\tCDS\t1653223\t1653750\t1\t-\t0\ttranscript_id \"g22602.t1\"; gene_id \"g22602\";\r\n", "5\t1653560\t1653562\t5\tAUGUSTUS\tCDS\t1653223\t1653750\t1\t-\t0\ttranscript_id \"g22602.t1\"; gene_id \"g22602\";\r\n", "5\t1653575\t1653577\t5\tAUGUSTUS\tCDS\t1653223\t1653750\t1\t-\t0\ttranscript_id \"g22602.t1\"; gene_id \"g22602\";\r\n", "5\t1653578\t1653580\t5\tAUGUSTUS\tCDS\t1653223\t1653750\t1\t-\t0\ttranscript_id \"g22602.t1\"; gene_id \"g22602\";\r\n", "5\t1653596\t1653598\t5\tAUGUSTUS\tCDS\t1653223\t1653750\t1\t-\t0\ttranscript_id \"g22602.t1\"; gene_id \"g22602\";\r\n", "5\t1653614\t1653616\t5\tAUGUSTUS\tCDS\t1653223\t1653750\t1\t-\t0\ttranscript_id \"g22602.t1\"; gene_id \"g22602\";\r\n", "\r\n", "==> Meth16_R1_001_val_1_bismark_bt2_pe._10x.bedgraph.bed-mcCDS <==\r\n", "2\t1704675\t1704677\t2\tAUGUSTUS\tCDS\t1704290\t1704742\t0.58\t-\t0\ttranscript_id \"g21949.t1\"; gene_id \"g21949\";\r\n", "2\t1704686\t1704688\t2\tAUGUSTUS\tCDS\t1704290\t1704742\t0.58\t-\t0\ttranscript_id \"g21949.t1\"; gene_id \"g21949\";\r\n", "2\t1704736\t1704738\t2\tAUGUSTUS\tCDS\t1704290\t1704742\t0.58\t-\t0\ttranscript_id \"g21949.t1\"; gene_id \"g21949\";\r\n", "2\t1984196\t1984198\t2\tAUGUSTUS\tCDS\t1983612\t1984280\t0.89\t-\t0\ttranscript_id \"g21974.t1\"; gene_id \"g21974\";\r\n", "2\t1984223\t1984225\t2\tAUGUSTUS\tCDS\t1983612\t1984280\t0.89\t-\t0\ttranscript_id \"g21974.t1\"; gene_id \"g21974\";\r\n", "2\t1984257\t1984259\t2\tAUGUSTUS\tCDS\t1983612\t1984280\t0.89\t-\t0\ttranscript_id \"g21974.t1\"; gene_id \"g21974\";\r\n", "2\t3036148\t3036150\t2\tAUGUSTUS\tCDS\t3036135\t3036719\t0.61\t+\t0\ttranscript_id \"g22168.t1\"; gene_id \"g22168\";\r\n", "2\t3036160\t3036162\t2\tAUGUSTUS\tCDS\t3036135\t3036719\t0.61\t+\t0\ttranscript_id \"g22168.t1\"; gene_id \"g22168\";\r\n", "2\t3036163\t3036165\t2\tAUGUSTUS\tCDS\t3036135\t3036719\t0.61\t+\t0\ttranscript_id \"g22168.t1\"; gene_id \"g22168\";\r\n", "2\t3036512\t3036514\t2\tAUGUSTUS\tCDS\t3036135\t3036719\t0.61\t+\t0\ttranscript_id \"g22168.t1\"; gene_id \"g22168\";\r\n", "\r\n", "==> Meth17_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-Meth.bed-mcCDS <==\r\n", "2\t3037511\t3037513\t2\tAUGUSTUS\tCDS\t3037241\t3037690\t1\t-\t0\ttranscript_id \"g22169.t1\"; gene_id \"g22169\";\r\n", "2\t3037528\t3037530\t2\tAUGUSTUS\tCDS\t3037241\t3037690\t1\t-\t0\ttranscript_id \"g22169.t1\"; gene_id \"g22169\";\r\n", "6\t2128294\t2128296\t6\tAUGUSTUS\tCDS\t2127224\t2129603\t0.7\t-\t0\ttranscript_id \"g22812.t1\"; gene_id \"g22812\";\r\n", "6\t2128304\t2128306\t6\tAUGUSTUS\tCDS\t2127224\t2129603\t0.7\t-\t0\ttranscript_id \"g22812.t1\"; gene_id \"g22812\";\r\n", "6\t2128347\t2128349\t6\tAUGUSTUS\tCDS\t2127224\t2129603\t0.7\t-\t0\ttranscript_id \"g22812.t1\"; gene_id \"g22812\";\r\n", "10\t733041\t733043\t10\tAUGUSTUS\tCDS\t732999\t733374\t1\t-\t1\ttranscript_id \"g23342.t1\"; gene_id \"g23342\";\r\n", "10\t733045\t733047\t10\tAUGUSTUS\tCDS\t732999\t733374\t1\t-\t1\ttranscript_id \"g23342.t1\"; gene_id \"g23342\";\r\n", "10\t733051\t733053\t10\tAUGUSTUS\tCDS\t732999\t733374\t1\t-\t1\ttranscript_id \"g23342.t1\"; gene_id \"g23342\";\r\n", "10\t733081\t733083\t10\tAUGUSTUS\tCDS\t732999\t733374\t1\t-\t1\ttranscript_id \"g23342.t1\"; gene_id \"g23342\";\r\n", "10\t733091\t733093\t10\tAUGUSTUS\tCDS\t732999\t733374\t1\t-\t1\ttranscript_id \"g23342.t1\"; gene_id \"g23342\";\r\n", "\r\n", "==> Meth17_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-sparseMeth.bed-mcCDS <==\r\n", "9\t23708\t23710\t9\tAUGUSTUS\tCDS\t23704\t24276\t1\t+\t0\ttranscript_id \"g23074.t1\"; gene_id \"g23074\";\r\n", "9\t23768\t23770\t9\tAUGUSTUS\tCDS\t23704\t24276\t1\t+\t0\ttranscript_id \"g23074.t1\"; gene_id \"g23074\";\r\n", "9\t23821\t23823\t9\tAUGUSTUS\tCDS\t23704\t24276\t1\t+\t0\ttranscript_id \"g23074.t1\"; gene_id \"g23074\";\r\n", "9\t23824\t23826\t9\tAUGUSTUS\tCDS\t23704\t24276\t1\t+\t0\ttranscript_id \"g23074.t1\"; gene_id \"g23074\";\r\n", "9\t23837\t23839\t9\tAUGUSTUS\tCDS\t23704\t24276\t1\t+\t0\ttranscript_id \"g23074.t1\"; gene_id \"g23074\";\r\n", "10\t40767\t40769\t10\tAUGUSTUS\tCDS\t40495\t40965\t0.34\t-\t0\ttranscript_id \"g23272.t1\"; gene_id \"g23272\";\r\n", "10\t40775\t40777\t10\tAUGUSTUS\tCDS\t40495\t40965\t0.34\t-\t0\ttranscript_id \"g23272.t1\"; gene_id \"g23272\";\r\n", "10\t40787\t40789\t10\tAUGUSTUS\tCDS\t40495\t40965\t0.34\t-\t0\ttranscript_id \"g23272.t1\"; gene_id \"g23272\";\r\n", "10\t40803\t40805\t10\tAUGUSTUS\tCDS\t40495\t40965\t0.34\t-\t0\ttranscript_id \"g23272.t1\"; gene_id \"g23272\";\r\n", "10\t40832\t40834\t10\tAUGUSTUS\tCDS\t40495\t40965\t0.34\t-\t0\ttranscript_id \"g23272.t1\"; gene_id \"g23272\";\r\n", "\r\n", "==> Meth17_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-unMeth.bed-mcCDS <==\r\n", "1\t832598\t832600\t1\tAUGUSTUS\tCDS\t830085\t836441\t1\t-\t2\ttranscript_id \"g21601.t1\"; gene_id \"g21601\";\r\n", "4\t1192766\t1192768\t4\tAUGUSTUS\tCDS\t1192714\t1192774\t1\t+\t0\ttranscript_id \"g22353.t1\"; gene_id \"g22353\";\r\n", "9\t23774\t23776\t9\tAUGUSTUS\tCDS\t23704\t24276\t1\t+\t0\ttranscript_id \"g23074.t1\"; gene_id \"g23074\";\r\n", "9\t23787\t23789\t9\tAUGUSTUS\tCDS\t23704\t24276\t1\t+\t0\ttranscript_id \"g23074.t1\"; gene_id \"g23074\";\r\n", "9\t23827\t23829\t9\tAUGUSTUS\tCDS\t23704\t24276\t1\t+\t0\ttranscript_id \"g23074.t1\"; gene_id \"g23074\";\r\n", "9\t23832\t23834\t9\tAUGUSTUS\tCDS\t23704\t24276\t1\t+\t0\ttranscript_id \"g23074.t1\"; gene_id \"g23074\";\r\n", "10\t40769\t40771\t10\tAUGUSTUS\tCDS\t40495\t40965\t0.34\t-\t0\ttranscript_id \"g23272.t1\"; gene_id \"g23272\";\r\n", "10\t40784\t40786\t10\tAUGUSTUS\tCDS\t40495\t40965\t0.34\t-\t0\ttranscript_id \"g23272.t1\"; gene_id \"g23272\";\r\n", "10\t40798\t40800\t10\tAUGUSTUS\tCDS\t40495\t40965\t0.34\t-\t0\ttranscript_id \"g23272.t1\"; gene_id \"g23272\";\r\n", "10\t40813\t40815\t10\tAUGUSTUS\tCDS\t40495\t40965\t0.34\t-\t0\ttranscript_id \"g23272.t1\"; gene_id \"g23272\";\r\n", "\r\n", "==> Meth17_R1_001_val_1_bismark_bt2_pe._10x.bedgraph.bed-mcCDS <==\r\n", "1\t832598\t832600\t1\tAUGUSTUS\tCDS\t830085\t836441\t1\t-\t2\ttranscript_id \"g21601.t1\"; gene_id \"g21601\";\r\n", "2\t3037511\t3037513\t2\tAUGUSTUS\tCDS\t3037241\t3037690\t1\t-\t0\ttranscript_id \"g22169.t1\"; gene_id \"g22169\";\r\n", "2\t3037528\t3037530\t2\tAUGUSTUS\tCDS\t3037241\t3037690\t1\t-\t0\ttranscript_id \"g22169.t1\"; gene_id \"g22169\";\r\n", "4\t1192766\t1192768\t4\tAUGUSTUS\tCDS\t1192714\t1192774\t1\t+\t0\ttranscript_id \"g22353.t1\"; gene_id \"g22353\";\r\n", "6\t2128294\t2128296\t6\tAUGUSTUS\tCDS\t2127224\t2129603\t0.7\t-\t0\ttranscript_id \"g22812.t1\"; gene_id \"g22812\";\r\n", "6\t2128304\t2128306\t6\tAUGUSTUS\tCDS\t2127224\t2129603\t0.7\t-\t0\ttranscript_id \"g22812.t1\"; gene_id \"g22812\";\r\n", "6\t2128347\t2128349\t6\tAUGUSTUS\tCDS\t2127224\t2129603\t0.7\t-\t0\ttranscript_id \"g22812.t1\"; gene_id \"g22812\";\r\n", "9\t23708\t23710\t9\tAUGUSTUS\tCDS\t23704\t24276\t1\t+\t0\ttranscript_id \"g23074.t1\"; gene_id \"g23074\";\r\n", "9\t23768\t23770\t9\tAUGUSTUS\tCDS\t23704\t24276\t1\t+\t0\ttranscript_id \"g23074.t1\"; gene_id \"g23074\";\r\n", "9\t23774\t23776\t9\tAUGUSTUS\tCDS\t23704\t24276\t1\t+\t0\ttranscript_id \"g23074.t1\"; gene_id \"g23074\";\r\n", "\r\n", "==> Meth18_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-Meth.bed-mcCDS <==\r\n", "1\t3129772\t3129774\t1\tAUGUSTUS\tCDS\t3129418\t3129828\t1\t+\t0\ttranscript_id \"g21754.t1\"; gene_id \"g21754\";\r\n", "1\t3129793\t3129795\t1\tAUGUSTUS\tCDS\t3129418\t3129828\t1\t+\t0\ttranscript_id \"g21754.t1\"; gene_id \"g21754\";\r\n", "1\t3129805\t3129807\t1\tAUGUSTUS\tCDS\t3129418\t3129828\t1\t+\t0\ttranscript_id \"g21754.t1\"; gene_id \"g21754\";\r\n", "6\t2130774\t2130776\t6\tAUGUSTUS\tCDS\t2130724\t2130850\t0.5\t-\t0\ttranscript_id \"g22813.t1\"; gene_id \"g22813\";\r\n", "10\t733001\t733003\t10\tAUGUSTUS\tCDS\t732999\t733374\t1\t-\t1\ttranscript_id \"g23342.t1\"; gene_id \"g23342\";\r\n", "10\t733024\t733026\t10\tAUGUSTUS\tCDS\t732999\t733374\t1\t-\t1\ttranscript_id \"g23342.t1\"; gene_id \"g23342\";\r\n", "10\t733030\t733032\t10\tAUGUSTUS\tCDS\t732999\t733374\t1\t-\t1\ttranscript_id \"g23342.t1\"; gene_id \"g23342\";\r\n", "10\t733037\t733039\t10\tAUGUSTUS\tCDS\t732999\t733374\t1\t-\t1\ttranscript_id \"g23342.t1\"; gene_id \"g23342\";\r\n", "10\t733041\t733043\t10\tAUGUSTUS\tCDS\t732999\t733374\t1\t-\t1\ttranscript_id \"g23342.t1\"; gene_id \"g23342\";\r\n", "10\t733045\t733047\t10\tAUGUSTUS\tCDS\t732999\t733374\t1\t-\t1\ttranscript_id \"g23342.t1\"; gene_id \"g23342\";\r\n", "\r\n", "==> Meth18_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-sparseMeth.bed-mcCDS <==\r\n", "18\t1159899\t1159901\t18\tAUGUSTUS\tCDS\t1159413\t1160108\t0.86\t+\t2\ttranscript_id \"g24521.t1\"; gene_id \"g24521\";\r\n", "18\t1472691\t1472693\t18\tAUGUSTUS\tCDS\t1472674\t1473061\t1\t+\t0\ttranscript_id \"g24547.t1\"; gene_id \"g24547\";\r\n", "18\t1472704\t1472706\t18\tAUGUSTUS\tCDS\t1472674\t1473061\t1\t+\t0\ttranscript_id \"g24547.t1\"; gene_id \"g24547\";\r\n", "18\t1472710\t1472712\t18\tAUGUSTUS\tCDS\t1472674\t1473061\t1\t+\t0\ttranscript_id \"g24547.t1\"; gene_id \"g24547\";\r\n", "18\t1472714\t1472716\t18\tAUGUSTUS\tCDS\t1472674\t1473061\t1\t+\t0\ttranscript_id \"g24547.t1\"; gene_id \"g24547\";\r\n", "21\t1329413\t1329415\t21\tAUGUSTUS\tCDS\t1328777\t1329764\t0.52\t-\t0\ttranscript_id \"g25222.t1\"; gene_id \"g25222\";\r\n", "35\t996357\t996359\t35\tAUGUSTUS\tCDS\t995460\t996936\t1\t+\t1\ttranscript_id \"g27130.t1\"; gene_id \"g27130\";\r\n", "59\t479268\t479270\t59\tAUGUSTUS\tCDS\t479141\t479609\t0.58\t+\t0\ttranscript_id \"g29850.t1\"; gene_id \"g29850\";\r\n", "59\t479294\t479296\t59\tAUGUSTUS\tCDS\t479141\t479609\t0.58\t+\t0\ttranscript_id \"g29850.t1\"; gene_id \"g29850\";\r\n", "59\t479296\t479298\t59\tAUGUSTUS\tCDS\t479141\t479609\t0.58\t+\t0\ttranscript_id \"g29850.t1\"; gene_id \"g29850\";\r\n", "\r\n", "==> Meth18_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-unMeth.bed-mcCDS <==\r\n", "4\t1572709\t1572711\t4\tAUGUSTUS\tCDS\t1572126\t1573771\t0.59\t-\t1\ttranscript_id \"g22382.t1\"; gene_id \"g22382\";\r\n", "4\t1572728\t1572730\t4\tAUGUSTUS\tCDS\t1572126\t1573771\t0.59\t-\t1\ttranscript_id \"g22382.t1\"; gene_id \"g22382\";\r\n", "6\t1708611\t1708613\t6\tAUGUSTUS\tCDS\t1705256\t1708818\t0.58\t+\t2\ttranscript_id \"g22787.t1\"; gene_id \"g22787\";\r\n", "6\t1708625\t1708627\t6\tAUGUSTUS\tCDS\t1705256\t1708818\t0.58\t+\t2\ttranscript_id \"g22787.t1\"; gene_id \"g22787\";\r\n", "10\t733258\t733260\t10\tAUGUSTUS\tCDS\t732999\t733374\t1\t-\t1\ttranscript_id \"g23342.t1\"; gene_id \"g23342\";\r\n", "18\t1159716\t1159718\t18\tAUGUSTUS\tCDS\t1159413\t1160108\t0.86\t+\t2\ttranscript_id \"g24521.t1\"; gene_id \"g24521\";\r\n", "18\t1159755\t1159757\t18\tAUGUSTUS\tCDS\t1159413\t1160108\t0.86\t+\t2\ttranscript_id \"g24521.t1\"; gene_id \"g24521\";\r\n", "18\t1159836\t1159838\t18\tAUGUSTUS\tCDS\t1159413\t1160108\t0.86\t+\t2\ttranscript_id \"g24521.t1\"; gene_id \"g24521\";\r\n", "18\t1159839\t1159841\t18\tAUGUSTUS\tCDS\t1159413\t1160108\t0.86\t+\t2\ttranscript_id \"g24521.t1\"; gene_id \"g24521\";\r\n", "18\t1159842\t1159844\t18\tAUGUSTUS\tCDS\t1159413\t1160108\t0.86\t+\t2\ttranscript_id \"g24521.t1\"; gene_id \"g24521\";\r\n", "\r\n", "==> Meth18_R1_001_val_1_bismark_bt2_pe._10x.bedgraph.bed-mcCDS <==\r\n", "1\t3129772\t3129774\t1\tAUGUSTUS\tCDS\t3129418\t3129828\t1\t+\t0\ttranscript_id \"g21754.t1\"; gene_id \"g21754\";\r\n", "1\t3129793\t3129795\t1\tAUGUSTUS\tCDS\t3129418\t3129828\t1\t+\t0\ttranscript_id \"g21754.t1\"; gene_id \"g21754\";\r\n", "1\t3129805\t3129807\t1\tAUGUSTUS\tCDS\t3129418\t3129828\t1\t+\t0\ttranscript_id \"g21754.t1\"; gene_id \"g21754\";\r\n", "4\t1572709\t1572711\t4\tAUGUSTUS\tCDS\t1572126\t1573771\t0.59\t-\t1\ttranscript_id \"g22382.t1\"; gene_id \"g22382\";\r\n", "4\t1572728\t1572730\t4\tAUGUSTUS\tCDS\t1572126\t1573771\t0.59\t-\t1\ttranscript_id \"g22382.t1\"; gene_id \"g22382\";\r\n", "6\t1708611\t1708613\t6\tAUGUSTUS\tCDS\t1705256\t1708818\t0.58\t+\t2\ttranscript_id \"g22787.t1\"; gene_id \"g22787\";\r\n", "6\t1708625\t1708627\t6\tAUGUSTUS\tCDS\t1705256\t1708818\t0.58\t+\t2\ttranscript_id \"g22787.t1\"; gene_id \"g22787\";\r\n", "6\t2130774\t2130776\t6\tAUGUSTUS\tCDS\t2130724\t2130850\t0.5\t-\t0\ttranscript_id \"g22813.t1\"; gene_id \"g22813\";\r\n", "10\t733001\t733003\t10\tAUGUSTUS\tCDS\t732999\t733374\t1\t-\t1\ttranscript_id \"g23342.t1\"; gene_id \"g23342\";\r\n", "10\t733024\t733026\t10\tAUGUSTUS\tCDS\t732999\t733374\t1\t-\t1\ttranscript_id \"g23342.t1\"; gene_id \"g23342\";\r\n" ] } ], "source": [ "#Check output\n", "!head *mcCDS" ] }, { "cell_type": "code", "execution_count": 54, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ " 5918 Meth10_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-Meth.bed-mcCDS\n", " 7652 Meth10_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-sparseMeth.bed-mcCDS\n", " 50048 Meth10_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-unMeth.bed-mcCDS\n", " 63618 Meth10_R1_001_val_1_bismark_bt2_pe._10x.bedgraph.bed-mcCDS\n", " 8085 Meth11_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-Meth.bed-mcCDS\n", " 7257 Meth11_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-sparseMeth.bed-mcCDS\n", " 51737 Meth11_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-unMeth.bed-mcCDS\n", " 67079 Meth11_R1_001_val_1_bismark_bt2_pe._10x.bedgraph.bed-mcCDS\n", " 25530 Meth12_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-Meth.bed-mcCDS\n", " 16812 Meth12_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-sparseMeth.bed-mcCDS\n", " 166759 Meth12_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-unMeth.bed-mcCDS\n", " 209101 Meth12_R1_001_val_1_bismark_bt2_pe._10x.bedgraph.bed-mcCDS\n", " 14708 Meth13_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-Meth.bed-mcCDS\n", " 10382 Meth13_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-sparseMeth.bed-mcCDS\n", " 165162 Meth13_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-unMeth.bed-mcCDS\n", " 190252 Meth13_R1_001_val_1_bismark_bt2_pe._10x.bedgraph.bed-mcCDS\n", " 9279 Meth14_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-Meth.bed-mcCDS\n", " 8654 Meth14_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-sparseMeth.bed-mcCDS\n", " 133766 Meth14_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-unMeth.bed-mcCDS\n", " 151699 Meth14_R1_001_val_1_bismark_bt2_pe._10x.bedgraph.bed-mcCDS\n", " 11132 Meth15_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-Meth.bed-mcCDS\n", " 12318 Meth15_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-sparseMeth.bed-mcCDS\n", " 163427 Meth15_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-unMeth.bed-mcCDS\n", " 186877 Meth15_R1_001_val_1_bismark_bt2_pe._10x.bedgraph.bed-mcCDS\n", " 2046 Meth16_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-Meth.bed-mcCDS\n", " 623 Meth16_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-sparseMeth.bed-mcCDS\n", " 1995 Meth16_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-unMeth.bed-mcCDS\n", " 4664 Meth16_R1_001_val_1_bismark_bt2_pe._10x.bedgraph.bed-mcCDS\n", " 758 Meth17_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-Meth.bed-mcCDS\n", " 220 Meth17_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-sparseMeth.bed-mcCDS\n", " 1329 Meth17_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-unMeth.bed-mcCDS\n", " 2307 Meth17_R1_001_val_1_bismark_bt2_pe._10x.bedgraph.bed-mcCDS\n", " 750 Meth18_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-Meth.bed-mcCDS\n", " 93 Meth18_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-sparseMeth.bed-mcCDS\n", " 439 Meth18_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-unMeth.bed-mcCDS\n", " 1282 Meth18_R1_001_val_1_bismark_bt2_pe._10x.bedgraph.bed-mcCDS\n", " 1753758 total\n" ] } ], "source": [ "#Count number of overlaps\n", "!wc -l *mcCDS" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "#### 4d. Introns" ] }, { "cell_type": "code", "execution_count": 55, "metadata": { "collapsed": true, "scrolled": true }, "outputs": [], "source": [ "%%bash\n", "\n", "for f in *bed\n", "do\n", " /usr/local/bin/intersectBed \\\n", " -wb \\\n", " -a ${f} \\\n", " -b ../../../genome-feature-files/Mcap.GFFannotation.intron.gff \\\n", " > ${f}-mcIntrons\n", "done" ] }, { "cell_type": "code", "execution_count": 56, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "==> Meth10_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-Meth.bed-mcIntrons <==\r\n", "1\t876587\t876589\t1\tAUGUSTUS\tintron\t875789\t877365\t1\t+\t.\ttranscript_id \"g21603.t1\"; gene_id \"g21603\";\r\n", "1\t876606\t876608\t1\tAUGUSTUS\tintron\t875789\t877365\t1\t+\t.\ttranscript_id \"g21603.t1\"; gene_id \"g21603\";\r\n", "1\t1267992\t1267994\t1\tAUGUSTUS\tintron\t1266365\t1270850\t1\t-\t.\ttranscript_id \"g21628.t1\"; gene_id \"g21628\";\r\n", "1\t1269495\t1269497\t1\tAUGUSTUS\tintron\t1266365\t1270850\t1\t-\t.\ttranscript_id \"g21628.t1\"; gene_id \"g21628\";\r\n", "1\t1269508\t1269510\t1\tAUGUSTUS\tintron\t1266365\t1270850\t1\t-\t.\ttranscript_id \"g21628.t1\"; gene_id \"g21628\";\r\n", "1\t1269532\t1269534\t1\tAUGUSTUS\tintron\t1266365\t1270850\t1\t-\t.\ttranscript_id \"g21628.t1\"; gene_id \"g21628\";\r\n", "1\t1373604\t1373606\t1\tAUGUSTUS\tintron\t1372665\t1373781\t1\t-\t.\ttranscript_id \"g21633.t1\"; gene_id \"g21633\";\r\n", "1\t1387604\t1387606\t1\tAUGUSTUS\tintron\t1385589\t1390066\t1\t+\t.\ttranscript_id \"g21634.t1\"; gene_id \"g21634\";\r\n", "1\t1390056\t1390058\t1\tAUGUSTUS\tintron\t1385589\t1390066\t1\t+\t.\ttranscript_id \"g21634.t1\"; gene_id \"g21634\";\r\n", "1\t1408828\t1408830\t1\tAUGUSTUS\tintron\t1404360\t1409055\t1\t-\t.\ttranscript_id \"g21635.t1\"; gene_id \"g21635\";\r\n", "\r\n", "==> Meth10_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-sparseMeth.bed-mcIntrons <==\r\n", "1\t527701\t527703\t1\tAUGUSTUS\tintron\t527465\t530650\t1\t-\t.\ttranscript_id \"g21573.t1\"; gene_id \"g21573\";\r\n", "1\t527706\t527708\t1\tAUGUSTUS\tintron\t527465\t530650\t1\t-\t.\ttranscript_id \"g21573.t1\"; gene_id \"g21573\";\r\n", "1\t527726\t527728\t1\tAUGUSTUS\tintron\t527465\t530650\t1\t-\t.\ttranscript_id \"g21573.t1\"; gene_id \"g21573\";\r\n", "1\t527739\t527741\t1\tAUGUSTUS\tintron\t527465\t530650\t1\t-\t.\ttranscript_id \"g21573.t1\"; gene_id \"g21573\";\r\n", "1\t624562\t624564\t1\tAUGUSTUS\tintron\t623139\t628254\t1\t+\t.\ttranscript_id \"g21583.t1\"; gene_id \"g21583\";\r\n", "1\t847267\t847269\t1\tAUGUSTUS\tintron\t836442\t849586\t1\t-\t.\ttranscript_id \"g21601.t1\"; gene_id \"g21601\";\r\n", "1\t847366\t847368\t1\tAUGUSTUS\tintron\t836442\t849586\t1\t-\t.\ttranscript_id \"g21601.t1\"; gene_id \"g21601\";\r\n", "1\t847374\t847376\t1\tAUGUSTUS\tintron\t836442\t849586\t1\t-\t.\ttranscript_id \"g21601.t1\"; gene_id \"g21601\";\r\n", "1\t847762\t847764\t1\tAUGUSTUS\tintron\t836442\t849586\t1\t-\t.\ttranscript_id \"g21601.t1\"; gene_id \"g21601\";\r\n", "1\t918080\t918082\t1\tAUGUSTUS\tintron\t915729\t918741\t1\t+\t.\ttranscript_id \"g21603.t1\"; gene_id \"g21603\";\r\n", "\r\n", "==> Meth10_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-unMeth.bed-mcIntrons <==\r\n", "1\t323150\t323152\t1\tAUGUSTUS\tintron\t323104\t325589\t1\t-\t.\ttranscript_id \"g21554.t1\"; gene_id \"g21554\";\r\n", "1\t323157\t323159\t1\tAUGUSTUS\tintron\t323104\t325589\t1\t-\t.\ttranscript_id \"g21554.t1\"; gene_id \"g21554\";\r\n", "1\t323172\t323174\t1\tAUGUSTUS\tintron\t323104\t325589\t1\t-\t.\ttranscript_id \"g21554.t1\"; gene_id \"g21554\";\r\n", "1\t323177\t323179\t1\tAUGUSTUS\tintron\t323104\t325589\t1\t-\t.\ttranscript_id \"g21554.t1\"; gene_id \"g21554\";\r\n", "1\t323190\t323192\t1\tAUGUSTUS\tintron\t323104\t325589\t1\t-\t.\ttranscript_id \"g21554.t1\"; gene_id \"g21554\";\r\n", "1\t323320\t323322\t1\tAUGUSTUS\tintron\t323104\t325589\t1\t-\t.\ttranscript_id \"g21554.t1\"; gene_id \"g21554\";\r\n", "1\t323396\t323398\t1\tAUGUSTUS\tintron\t323104\t325589\t1\t-\t.\ttranscript_id \"g21554.t1\"; gene_id \"g21554\";\r\n", "1\t323429\t323431\t1\tAUGUSTUS\tintron\t323104\t325589\t1\t-\t.\ttranscript_id \"g21554.t1\"; gene_id \"g21554\";\r\n", "1\t323466\t323468\t1\tAUGUSTUS\tintron\t323104\t325589\t1\t-\t.\ttranscript_id \"g21554.t1\"; gene_id \"g21554\";\r\n", "1\t323487\t323489\t1\tAUGUSTUS\tintron\t323104\t325589\t1\t-\t.\ttranscript_id \"g21554.t1\"; gene_id \"g21554\";\r\n", "\r\n", "==> Meth10_R1_001_val_1_bismark_bt2_pe._10x.bedgraph.bed-mcIntrons <==\r\n", "1\t323150\t323152\t1\tAUGUSTUS\tintron\t323104\t325589\t1\t-\t.\ttranscript_id \"g21554.t1\"; gene_id \"g21554\";\r\n", "1\t323157\t323159\t1\tAUGUSTUS\tintron\t323104\t325589\t1\t-\t.\ttranscript_id \"g21554.t1\"; gene_id \"g21554\";\r\n", "1\t323172\t323174\t1\tAUGUSTUS\tintron\t323104\t325589\t1\t-\t.\ttranscript_id \"g21554.t1\"; gene_id \"g21554\";\r\n", "1\t323177\t323179\t1\tAUGUSTUS\tintron\t323104\t325589\t1\t-\t.\ttranscript_id \"g21554.t1\"; gene_id \"g21554\";\r\n", "1\t323190\t323192\t1\tAUGUSTUS\tintron\t323104\t325589\t1\t-\t.\ttranscript_id \"g21554.t1\"; gene_id \"g21554\";\r\n", "1\t323320\t323322\t1\tAUGUSTUS\tintron\t323104\t325589\t1\t-\t.\ttranscript_id \"g21554.t1\"; gene_id \"g21554\";\r\n", "1\t323396\t323398\t1\tAUGUSTUS\tintron\t323104\t325589\t1\t-\t.\ttranscript_id \"g21554.t1\"; gene_id \"g21554\";\r\n", "1\t323429\t323431\t1\tAUGUSTUS\tintron\t323104\t325589\t1\t-\t.\ttranscript_id \"g21554.t1\"; gene_id \"g21554\";\r\n", "1\t323466\t323468\t1\tAUGUSTUS\tintron\t323104\t325589\t1\t-\t.\ttranscript_id \"g21554.t1\"; gene_id \"g21554\";\r\n", "1\t323487\t323489\t1\tAUGUSTUS\tintron\t323104\t325589\t1\t-\t.\ttranscript_id \"g21554.t1\"; gene_id \"g21554\";\r\n", "\r\n", "==> Meth11_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-Meth.bed-mcIntrons <==\r\n", "1\t1269495\t1269497\t1\tAUGUSTUS\tintron\t1266365\t1270850\t1\t-\t.\ttranscript_id \"g21628.t1\"; gene_id \"g21628\";\r\n", "1\t1269508\t1269510\t1\tAUGUSTUS\tintron\t1266365\t1270850\t1\t-\t.\ttranscript_id \"g21628.t1\"; gene_id \"g21628\";\r\n", "1\t1269532\t1269534\t1\tAUGUSTUS\tintron\t1266365\t1270850\t1\t-\t.\ttranscript_id \"g21628.t1\"; gene_id \"g21628\";\r\n", "1\t1273421\t1273423\t1\tAUGUSTUS\tintron\t1271431\t1276721\t1\t-\t.\ttranscript_id \"g21628.t1\"; gene_id \"g21628\";\r\n", "1\t1273455\t1273457\t1\tAUGUSTUS\tintron\t1271431\t1276721\t1\t-\t.\ttranscript_id \"g21628.t1\"; gene_id \"g21628\";\r\n", "1\t1273463\t1273465\t1\tAUGUSTUS\tintron\t1271431\t1276721\t1\t-\t.\ttranscript_id \"g21628.t1\"; gene_id \"g21628\";\r\n", "1\t1338202\t1338204\t1\tAUGUSTUS\tintron\t1336344\t1338646\t1\t-\t.\ttranscript_id \"g21630.t1\"; gene_id \"g21630\";\r\n", "1\t1338258\t1338260\t1\tAUGUSTUS\tintron\t1336344\t1338646\t1\t-\t.\ttranscript_id \"g21630.t1\"; gene_id \"g21630\";\r\n", "1\t1338275\t1338277\t1\tAUGUSTUS\tintron\t1336344\t1338646\t1\t-\t.\ttranscript_id \"g21630.t1\"; gene_id \"g21630\";\r\n", "1\t1372728\t1372730\t1\tAUGUSTUS\tintron\t1372665\t1373781\t1\t-\t.\ttranscript_id \"g21633.t1\"; gene_id \"g21633\";\r\n", "\r\n", "==> Meth11_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-sparseMeth.bed-mcIntrons <==\r\n", "1\t1131883\t1131885\t1\tAUGUSTUS\tintron\t1131317\t1132081\t0.91\t+\t.\ttranscript_id \"g21620.t1\"; gene_id \"g21620\";\r\n", "1\t1131892\t1131894\t1\tAUGUSTUS\tintron\t1131317\t1132081\t0.91\t+\t.\ttranscript_id \"g21620.t1\"; gene_id \"g21620\";\r\n", "1\t1237556\t1237558\t1\tAUGUSTUS\tintron\t1236985\t1238185\t1\t-\t.\ttranscript_id \"g21628.t1\"; gene_id \"g21628\";\r\n", "1\t1540360\t1540362\t1\tAUGUSTUS\tintron\t1534875\t1541508\t1\t+\t.\ttranscript_id \"g21645.t1\"; gene_id \"g21645\";\r\n", "1\t1540374\t1540376\t1\tAUGUSTUS\tintron\t1534875\t1541508\t1\t+\t.\ttranscript_id \"g21645.t1\"; gene_id \"g21645\";\r\n", "1\t1540500\t1540502\t1\tAUGUSTUS\tintron\t1534875\t1541508\t1\t+\t.\ttranscript_id \"g21645.t1\"; gene_id \"g21645\";\r\n", "1\t1540514\t1540516\t1\tAUGUSTUS\tintron\t1534875\t1541508\t1\t+\t.\ttranscript_id \"g21645.t1\"; gene_id \"g21645\";\r\n", "1\t1540520\t1540522\t1\tAUGUSTUS\tintron\t1534875\t1541508\t1\t+\t.\ttranscript_id \"g21645.t1\"; gene_id \"g21645\";\r\n", "1\t1540534\t1540536\t1\tAUGUSTUS\tintron\t1534875\t1541508\t1\t+\t.\ttranscript_id \"g21645.t1\"; gene_id \"g21645\";\r\n", "1\t1540574\t1540576\t1\tAUGUSTUS\tintron\t1534875\t1541508\t1\t+\t.\ttranscript_id \"g21645.t1\"; gene_id \"g21645\";\r\n", "\r\n", "==> Meth11_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-unMeth.bed-mcIntrons <==\r\n", "1\t323354\t323356\t1\tAUGUSTUS\tintron\t323104\t325589\t1\t-\t.\ttranscript_id \"g21554.t1\"; gene_id \"g21554\";\r\n", "1\t323373\t323375\t1\tAUGUSTUS\tintron\t323104\t325589\t1\t-\t.\ttranscript_id \"g21554.t1\"; gene_id \"g21554\";\r\n", "1\t323396\t323398\t1\tAUGUSTUS\tintron\t323104\t325589\t1\t-\t.\ttranscript_id \"g21554.t1\"; gene_id \"g21554\";\r\n", "1\t323429\t323431\t1\tAUGUSTUS\tintron\t323104\t325589\t1\t-\t.\ttranscript_id \"g21554.t1\"; gene_id \"g21554\";\r\n", "1\t323524\t323526\t1\tAUGUSTUS\tintron\t323104\t325589\t1\t-\t.\ttranscript_id \"g21554.t1\"; gene_id \"g21554\";\r\n", "1\t324840\t324842\t1\tAUGUSTUS\tintron\t323104\t325589\t1\t-\t.\ttranscript_id \"g21554.t1\"; gene_id \"g21554\";\r\n", "1\t324861\t324863\t1\tAUGUSTUS\tintron\t323104\t325589\t1\t-\t.\ttranscript_id \"g21554.t1\"; gene_id \"g21554\";\r\n", "1\t324874\t324876\t1\tAUGUSTUS\tintron\t323104\t325589\t1\t-\t.\ttranscript_id \"g21554.t1\"; gene_id \"g21554\";\r\n", "1\t324876\t324878\t1\tAUGUSTUS\tintron\t323104\t325589\t1\t-\t.\ttranscript_id \"g21554.t1\"; gene_id \"g21554\";\r\n", "1\t324888\t324890\t1\tAUGUSTUS\tintron\t323104\t325589\t1\t-\t.\ttranscript_id \"g21554.t1\"; gene_id \"g21554\";\r\n", "\r\n", "==> Meth11_R1_001_val_1_bismark_bt2_pe._10x.bedgraph.bed-mcIntrons <==\r\n", "1\t323354\t323356\t1\tAUGUSTUS\tintron\t323104\t325589\t1\t-\t.\ttranscript_id \"g21554.t1\"; gene_id \"g21554\";\r\n", "1\t323373\t323375\t1\tAUGUSTUS\tintron\t323104\t325589\t1\t-\t.\ttranscript_id \"g21554.t1\"; gene_id \"g21554\";\r\n", "1\t323396\t323398\t1\tAUGUSTUS\tintron\t323104\t325589\t1\t-\t.\ttranscript_id \"g21554.t1\"; gene_id \"g21554\";\r\n", "1\t323429\t323431\t1\tAUGUSTUS\tintron\t323104\t325589\t1\t-\t.\ttranscript_id \"g21554.t1\"; gene_id \"g21554\";\r\n", "1\t323524\t323526\t1\tAUGUSTUS\tintron\t323104\t325589\t1\t-\t.\ttranscript_id \"g21554.t1\"; gene_id \"g21554\";\r\n", "1\t324840\t324842\t1\tAUGUSTUS\tintron\t323104\t325589\t1\t-\t.\ttranscript_id \"g21554.t1\"; gene_id \"g21554\";\r\n", "1\t324861\t324863\t1\tAUGUSTUS\tintron\t323104\t325589\t1\t-\t.\ttranscript_id \"g21554.t1\"; gene_id \"g21554\";\r\n", "1\t324874\t324876\t1\tAUGUSTUS\tintron\t323104\t325589\t1\t-\t.\ttranscript_id \"g21554.t1\"; gene_id \"g21554\";\r\n", "1\t324876\t324878\t1\tAUGUSTUS\tintron\t323104\t325589\t1\t-\t.\ttranscript_id \"g21554.t1\"; gene_id \"g21554\";\r\n", "1\t324888\t324890\t1\tAUGUSTUS\tintron\t323104\t325589\t1\t-\t.\ttranscript_id \"g21554.t1\"; gene_id \"g21554\";\r\n", "\r\n", "==> Meth12_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-Meth.bed-mcIntrons <==\r\n", "1\t69151\t69153\t1\tAUGUSTUS\tintron\t67319\t71345\t1\t+\t.\ttranscript_id \"g21536.t1\"; gene_id \"g21536\";\r\n", "1\t69235\t69237\t1\tAUGUSTUS\tintron\t67319\t71345\t1\t+\t.\ttranscript_id \"g21536.t1\"; gene_id \"g21536\";\r\n", "1\t69580\t69582\t1\tAUGUSTUS\tintron\t67319\t71345\t1\t+\t.\ttranscript_id \"g21536.t1\"; gene_id \"g21536\";\r\n", "1\t69584\t69586\t1\tAUGUSTUS\tintron\t67319\t71345\t1\t+\t.\ttranscript_id \"g21536.t1\"; gene_id \"g21536\";\r\n", "1\t69845\t69847\t1\tAUGUSTUS\tintron\t67319\t71345\t1\t+\t.\ttranscript_id \"g21536.t1\"; gene_id \"g21536\";\r\n", "1\t69882\t69884\t1\tAUGUSTUS\tintron\t67319\t71345\t1\t+\t.\ttranscript_id \"g21536.t1\"; gene_id \"g21536\";\r\n", "1\t70019\t70021\t1\tAUGUSTUS\tintron\t67319\t71345\t1\t+\t.\ttranscript_id \"g21536.t1\"; gene_id \"g21536\";\r\n", "1\t70068\t70070\t1\tAUGUSTUS\tintron\t67319\t71345\t1\t+\t.\ttranscript_id \"g21536.t1\"; gene_id \"g21536\";\r\n", "1\t70083\t70085\t1\tAUGUSTUS\tintron\t67319\t71345\t1\t+\t.\ttranscript_id \"g21536.t1\"; gene_id \"g21536\";\r\n", "1\t70129\t70131\t1\tAUGUSTUS\tintron\t67319\t71345\t1\t+\t.\ttranscript_id \"g21536.t1\"; gene_id \"g21536\";\r\n", "\r\n", "==> Meth12_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-sparseMeth.bed-mcIntrons <==\r\n", "1\t79955\t79957\t1\tAUGUSTUS\tintron\t79128\t80295\t1\t+\t.\ttranscript_id \"g21536.t1\"; gene_id \"g21536\";\r\n", "1\t356393\t356395\t1\tAUGUSTUS\tintron\t354630\t356737\t1\t+\t.\ttranscript_id \"g21557.t1\"; gene_id \"g21557\";\r\n", "1\t624754\t624756\t1\tAUGUSTUS\tintron\t623139\t628254\t1\t+\t.\ttranscript_id \"g21583.t1\"; gene_id \"g21583\";\r\n", "1\t754293\t754295\t1\tAUGUSTUS\tintron\t753791\t755392\t1\t-\t.\ttranscript_id \"g21595.t1\"; gene_id \"g21595\";\r\n", "1\t754314\t754316\t1\tAUGUSTUS\tintron\t753791\t755392\t1\t-\t.\ttranscript_id \"g21595.t1\"; gene_id \"g21595\";\r\n", "1\t789736\t789738\t1\tAUGUSTUS\tintron\t789727\t790249\t0.68\t-\t.\ttranscript_id \"g21600.t1\"; gene_id \"g21600\";\r\n", "1\t904729\t904731\t1\tAUGUSTUS\tintron\t903039\t905882\t1\t+\t.\ttranscript_id \"g21603.t1\"; gene_id \"g21603\";\r\n", "1\t911905\t911907\t1\tAUGUSTUS\tintron\t911560\t912591\t1\t+\t.\ttranscript_id \"g21603.t1\"; gene_id \"g21603\";\r\n", "1\t911934\t911936\t1\tAUGUSTUS\tintron\t911560\t912591\t1\t+\t.\ttranscript_id \"g21603.t1\"; gene_id \"g21603\";\r\n", "1\t916811\t916813\t1\tAUGUSTUS\tintron\t915729\t918741\t1\t+\t.\ttranscript_id \"g21603.t1\"; gene_id \"g21603\";\r\n", "\r\n", "==> Meth12_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-unMeth.bed-mcIntrons <==\r\n", "1\t46025\t46027\t1\tAUGUSTUS\tintron\t45209\t46624\t1\t+\t.\ttranscript_id \"g21534.t1\"; gene_id \"g21534\";\r\n", "1\t49087\t49089\t1\tAUGUSTUS\tintron\t47273\t49942\t1\t+\t.\ttranscript_id \"g21534.t1\"; gene_id \"g21534\";\r\n", "1\t49093\t49095\t1\tAUGUSTUS\tintron\t47273\t49942\t1\t+\t.\ttranscript_id \"g21534.t1\"; gene_id \"g21534\";\r\n", "1\t49102\t49104\t1\tAUGUSTUS\tintron\t47273\t49942\t1\t+\t.\ttranscript_id \"g21534.t1\"; gene_id \"g21534\";\r\n", "1\t49119\t49121\t1\tAUGUSTUS\tintron\t47273\t49942\t1\t+\t.\ttranscript_id \"g21534.t1\"; gene_id \"g21534\";\r\n", "1\t49123\t49125\t1\tAUGUSTUS\tintron\t47273\t49942\t1\t+\t.\ttranscript_id \"g21534.t1\"; gene_id \"g21534\";\r\n", "1\t49169\t49171\t1\tAUGUSTUS\tintron\t47273\t49942\t1\t+\t.\ttranscript_id \"g21534.t1\"; gene_id \"g21534\";\r\n", "1\t49194\t49196\t1\tAUGUSTUS\tintron\t47273\t49942\t1\t+\t.\ttranscript_id \"g21534.t1\"; gene_id \"g21534\";\r\n", "1\t75386\t75388\t1\tAUGUSTUS\tintron\t74647\t75637\t1\t+\t.\ttranscript_id \"g21536.t1\"; gene_id \"g21536\";\r\n", "1\t75401\t75403\t1\tAUGUSTUS\tintron\t74647\t75637\t1\t+\t.\ttranscript_id \"g21536.t1\"; gene_id \"g21536\";\r\n", "\r\n", "==> Meth12_R1_001_val_1_bismark_bt2_pe._10x.bedgraph.bed-mcIntrons <==\r\n", "1\t46025\t46027\t1\tAUGUSTUS\tintron\t45209\t46624\t1\t+\t.\ttranscript_id \"g21534.t1\"; gene_id \"g21534\";\r\n", "1\t49087\t49089\t1\tAUGUSTUS\tintron\t47273\t49942\t1\t+\t.\ttranscript_id \"g21534.t1\"; gene_id \"g21534\";\r\n", "1\t49093\t49095\t1\tAUGUSTUS\tintron\t47273\t49942\t1\t+\t.\ttranscript_id \"g21534.t1\"; gene_id \"g21534\";\r\n", "1\t49102\t49104\t1\tAUGUSTUS\tintron\t47273\t49942\t1\t+\t.\ttranscript_id \"g21534.t1\"; gene_id \"g21534\";\r\n", "1\t49119\t49121\t1\tAUGUSTUS\tintron\t47273\t49942\t1\t+\t.\ttranscript_id \"g21534.t1\"; gene_id \"g21534\";\r\n", "1\t49123\t49125\t1\tAUGUSTUS\tintron\t47273\t49942\t1\t+\t.\ttranscript_id \"g21534.t1\"; gene_id \"g21534\";\r\n", "1\t49169\t49171\t1\tAUGUSTUS\tintron\t47273\t49942\t1\t+\t.\ttranscript_id \"g21534.t1\"; gene_id \"g21534\";\r\n", "1\t49194\t49196\t1\tAUGUSTUS\tintron\t47273\t49942\t1\t+\t.\ttranscript_id \"g21534.t1\"; gene_id \"g21534\";\r\n", "1\t69151\t69153\t1\tAUGUSTUS\tintron\t67319\t71345\t1\t+\t.\ttranscript_id \"g21536.t1\"; gene_id \"g21536\";\r\n", "1\t69235\t69237\t1\tAUGUSTUS\tintron\t67319\t71345\t1\t+\t.\ttranscript_id \"g21536.t1\"; gene_id \"g21536\";\r\n", "\r\n", "==> Meth13_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-Meth.bed-mcIntrons <==\r\n", "1\t80721\t80723\t1\tAUGUSTUS\tintron\t80701\t82492\t1\t+\t.\ttranscript_id \"g21536.t1\"; gene_id \"g21536\";\r\n", "1\t101462\t101464\t1\tAUGUSTUS\tintron\t100307\t102769\t1\t-\t.\ttranscript_id \"g21538.t1\"; gene_id \"g21538\";\r\n", "1\t101535\t101537\t1\tAUGUSTUS\tintron\t100307\t102769\t1\t-\t.\ttranscript_id \"g21538.t1\"; gene_id \"g21538\";\r\n", "1\t108331\t108333\t1\tAUGUSTUS\tintron\t104815\t109637\t1\t-\t.\ttranscript_id \"g21538.t1\"; gene_id \"g21538\";\r\n", "1\t108383\t108385\t1\tAUGUSTUS\tintron\t104815\t109637\t1\t-\t.\ttranscript_id \"g21538.t1\"; gene_id \"g21538\";\r\n", "1\t108427\t108429\t1\tAUGUSTUS\tintron\t104815\t109637\t1\t-\t.\ttranscript_id \"g21538.t1\"; gene_id \"g21538\";\r\n", "1\t108444\t108446\t1\tAUGUSTUS\tintron\t104815\t109637\t1\t-\t.\ttranscript_id \"g21538.t1\"; gene_id \"g21538\";\r\n", "1\t108465\t108467\t1\tAUGUSTUS\tintron\t104815\t109637\t1\t-\t.\ttranscript_id \"g21538.t1\"; gene_id \"g21538\";\r\n", "1\t108611\t108613\t1\tAUGUSTUS\tintron\t104815\t109637\t1\t-\t.\ttranscript_id \"g21538.t1\"; gene_id \"g21538\";\r\n", "1\t108629\t108631\t1\tAUGUSTUS\tintron\t104815\t109637\t1\t-\t.\ttranscript_id \"g21538.t1\"; gene_id \"g21538\";\r\n", "\r\n", "==> Meth13_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-sparseMeth.bed-mcIntrons <==\r\n", "1\t48370\t48372\t1\tAUGUSTUS\tintron\t47273\t49942\t1\t+\t.\ttranscript_id \"g21534.t1\"; gene_id \"g21534\";\r\n", "1\t332927\t332929\t1\tAUGUSTUS\tintron\t332879\t334068\t1\t-\t.\ttranscript_id \"g21555.t1\"; gene_id \"g21555\";\r\n", "1\t336069\t336071\t1\tAUGUSTUS\tintron\t334182\t338302\t1\t-\t.\ttranscript_id \"g21555.t1\"; gene_id \"g21555\";\r\n", "1\t336217\t336219\t1\tAUGUSTUS\tintron\t334182\t338302\t1\t-\t.\ttranscript_id \"g21555.t1\"; gene_id \"g21555\";\r\n", "1\t349633\t349635\t1\tAUGUSTUS\tintron\t349262\t351068\t1\t+\t.\ttranscript_id \"g21556.t1\"; gene_id \"g21556\";\r\n", "1\t369283\t369285\t1\tAUGUSTUS\tintron\t368880\t370580\t1\t-\t.\ttranscript_id \"g21558.t1\"; gene_id \"g21558\";\r\n", "1\t369679\t369681\t1\tAUGUSTUS\tintron\t368880\t370580\t1\t-\t.\ttranscript_id \"g21558.t1\"; gene_id \"g21558\";\r\n", "1\t372648\t372650\t1\tAUGUSTUS\tintron\t371951\t373926\t1\t-\t.\ttranscript_id \"g21558.t1\"; gene_id \"g21558\";\r\n", "1\t533612\t533614\t1\tAUGUSTUS\tintron\t532687\t534535\t1\t-\t.\ttranscript_id \"g21573.t1\"; gene_id \"g21573\";\r\n", "1\t626953\t626955\t1\tAUGUSTUS\tintron\t623139\t628254\t1\t+\t.\ttranscript_id \"g21583.t1\"; gene_id \"g21583\";\r\n", "\r\n", "==> Meth13_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-unMeth.bed-mcIntrons <==\r\n", "1\t23117\t23119\t1\tAUGUSTUS\tintron\t22609\t26300\t0.25\t-\t.\ttranscript_id \"g21533.t1\"; gene_id \"g21533\";\r\n", "1\t23139\t23141\t1\tAUGUSTUS\tintron\t22609\t26300\t0.25\t-\t.\ttranscript_id \"g21533.t1\"; gene_id \"g21533\";\r\n", "1\t23173\t23175\t1\tAUGUSTUS\tintron\t22609\t26300\t0.25\t-\t.\ttranscript_id \"g21533.t1\"; gene_id \"g21533\";\r\n", "1\t23202\t23204\t1\tAUGUSTUS\tintron\t22609\t26300\t0.25\t-\t.\ttranscript_id \"g21533.t1\"; gene_id \"g21533\";\r\n", "1\t23326\t23328\t1\tAUGUSTUS\tintron\t22609\t26300\t0.25\t-\t.\ttranscript_id \"g21533.t1\"; gene_id \"g21533\";\r\n", "1\t23334\t23336\t1\tAUGUSTUS\tintron\t22609\t26300\t0.25\t-\t.\ttranscript_id \"g21533.t1\"; gene_id \"g21533\";\r\n", "1\t23382\t23384\t1\tAUGUSTUS\tintron\t22609\t26300\t0.25\t-\t.\ttranscript_id \"g21533.t1\"; gene_id \"g21533\";\r\n", "1\t39477\t39479\t1\tAUGUSTUS\tintron\t37811\t45037\t1\t+\t.\ttranscript_id \"g21534.t1\"; gene_id \"g21534\";\r\n", "1\t39509\t39511\t1\tAUGUSTUS\tintron\t37811\t45037\t1\t+\t.\ttranscript_id \"g21534.t1\"; gene_id \"g21534\";\r\n", "1\t39552\t39554\t1\tAUGUSTUS\tintron\t37811\t45037\t1\t+\t.\ttranscript_id \"g21534.t1\"; gene_id \"g21534\";\r\n", "\r\n", "==> Meth13_R1_001_val_1_bismark_bt2_pe._10x.bedgraph.bed-mcIntrons <==\r\n", "1\t23117\t23119\t1\tAUGUSTUS\tintron\t22609\t26300\t0.25\t-\t.\ttranscript_id \"g21533.t1\"; gene_id \"g21533\";\r\n", "1\t23139\t23141\t1\tAUGUSTUS\tintron\t22609\t26300\t0.25\t-\t.\ttranscript_id \"g21533.t1\"; gene_id \"g21533\";\r\n", "1\t23173\t23175\t1\tAUGUSTUS\tintron\t22609\t26300\t0.25\t-\t.\ttranscript_id \"g21533.t1\"; gene_id \"g21533\";\r\n", "1\t23202\t23204\t1\tAUGUSTUS\tintron\t22609\t26300\t0.25\t-\t.\ttranscript_id \"g21533.t1\"; gene_id \"g21533\";\r\n", "1\t23326\t23328\t1\tAUGUSTUS\tintron\t22609\t26300\t0.25\t-\t.\ttranscript_id \"g21533.t1\"; gene_id \"g21533\";\r\n", "1\t23334\t23336\t1\tAUGUSTUS\tintron\t22609\t26300\t0.25\t-\t.\ttranscript_id \"g21533.t1\"; gene_id \"g21533\";\r\n", "1\t23382\t23384\t1\tAUGUSTUS\tintron\t22609\t26300\t0.25\t-\t.\ttranscript_id \"g21533.t1\"; gene_id \"g21533\";\r\n", "1\t39477\t39479\t1\tAUGUSTUS\tintron\t37811\t45037\t1\t+\t.\ttranscript_id \"g21534.t1\"; gene_id \"g21534\";\r\n", "1\t39509\t39511\t1\tAUGUSTUS\tintron\t37811\t45037\t1\t+\t.\ttranscript_id \"g21534.t1\"; gene_id \"g21534\";\r\n", "1\t39552\t39554\t1\tAUGUSTUS\tintron\t37811\t45037\t1\t+\t.\ttranscript_id \"g21534.t1\"; gene_id \"g21534\";\r\n", "\r\n", "==> Meth14_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-Meth.bed-mcIntrons <==\r\n", "1\t336217\t336219\t1\tAUGUSTUS\tintron\t334182\t338302\t1\t-\t.\ttranscript_id \"g21555.t1\"; gene_id \"g21555\";\r\n", "1\t527701\t527703\t1\tAUGUSTUS\tintron\t527465\t530650\t1\t-\t.\ttranscript_id \"g21573.t1\"; gene_id \"g21573\";\r\n", "1\t759941\t759943\t1\tAUGUSTUS\tintron\t757619\t761825\t1\t-\t.\ttranscript_id \"g21595.t1\"; gene_id \"g21595\";\r\n", "1\t759954\t759956\t1\tAUGUSTUS\tintron\t757619\t761825\t1\t-\t.\ttranscript_id \"g21595.t1\"; gene_id \"g21595\";\r\n", "1\t759983\t759985\t1\tAUGUSTUS\tintron\t757619\t761825\t1\t-\t.\ttranscript_id \"g21595.t1\"; gene_id \"g21595\";\r\n", "1\t759985\t759987\t1\tAUGUSTUS\tintron\t757619\t761825\t1\t-\t.\ttranscript_id \"g21595.t1\"; gene_id \"g21595\";\r\n", "1\t759994\t759996\t1\tAUGUSTUS\tintron\t757619\t761825\t1\t-\t.\ttranscript_id \"g21595.t1\"; gene_id \"g21595\";\r\n", "1\t760014\t760016\t1\tAUGUSTUS\tintron\t757619\t761825\t1\t-\t.\ttranscript_id \"g21595.t1\"; gene_id \"g21595\";\r\n", "1\t760023\t760025\t1\tAUGUSTUS\tintron\t757619\t761825\t1\t-\t.\ttranscript_id \"g21595.t1\"; gene_id \"g21595\";\r\n", "1\t760030\t760032\t1\tAUGUSTUS\tintron\t757619\t761825\t1\t-\t.\ttranscript_id \"g21595.t1\"; gene_id \"g21595\";\r\n", "\r\n", "==> Meth14_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-sparseMeth.bed-mcIntrons <==\r\n", "1\t323888\t323890\t1\tAUGUSTUS\tintron\t323104\t325589\t1\t-\t.\ttranscript_id \"g21554.t1\"; gene_id \"g21554\";\r\n", "1\t336069\t336071\t1\tAUGUSTUS\tintron\t334182\t338302\t1\t-\t.\ttranscript_id \"g21555.t1\"; gene_id \"g21555\";\r\n", "1\t344217\t344219\t1\tAUGUSTUS\tintron\t341159\t344880\t1\t-\t.\ttranscript_id \"g21555.t1\"; gene_id \"g21555\";\r\n", "1\t349633\t349635\t1\tAUGUSTUS\tintron\t349262\t351068\t1\t+\t.\ttranscript_id \"g21556.t1\"; gene_id \"g21556\";\r\n", "1\t367234\t367236\t1\tAUGUSTUS\tintron\t363572\t368794\t0.7\t-\t.\ttranscript_id \"g21558.t1\"; gene_id \"g21558\";\r\n", "1\t527706\t527708\t1\tAUGUSTUS\tintron\t527465\t530650\t1\t-\t.\ttranscript_id \"g21573.t1\"; gene_id \"g21573\";\r\n", "1\t527726\t527728\t1\tAUGUSTUS\tintron\t527465\t530650\t1\t-\t.\ttranscript_id \"g21573.t1\"; gene_id \"g21573\";\r\n", "1\t527739\t527741\t1\tAUGUSTUS\tintron\t527465\t530650\t1\t-\t.\ttranscript_id \"g21573.t1\"; gene_id \"g21573\";\r\n", "1\t527799\t527801\t1\tAUGUSTUS\tintron\t527465\t530650\t1\t-\t.\ttranscript_id \"g21573.t1\"; gene_id \"g21573\";\r\n", "1\t748661\t748663\t1\tAUGUSTUS\tintron\t748419\t750355\t0.98\t-\t.\ttranscript_id \"g21595.t1\"; gene_id \"g21595\";\r\n", "\r\n", "==> Meth14_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-unMeth.bed-mcIntrons <==\r\n", "1\t40450\t40452\t1\tAUGUSTUS\tintron\t37811\t45037\t1\t+\t.\ttranscript_id \"g21534.t1\"; gene_id \"g21534\";\r\n", "1\t40486\t40488\t1\tAUGUSTUS\tintron\t37811\t45037\t1\t+\t.\ttranscript_id \"g21534.t1\"; gene_id \"g21534\";\r\n", "1\t40541\t40543\t1\tAUGUSTUS\tintron\t37811\t45037\t1\t+\t.\ttranscript_id \"g21534.t1\"; gene_id \"g21534\";\r\n", "1\t40552\t40554\t1\tAUGUSTUS\tintron\t37811\t45037\t1\t+\t.\ttranscript_id \"g21534.t1\"; gene_id \"g21534\";\r\n", "1\t40555\t40557\t1\tAUGUSTUS\tintron\t37811\t45037\t1\t+\t.\ttranscript_id \"g21534.t1\"; gene_id \"g21534\";\r\n", "1\t44922\t44924\t1\tAUGUSTUS\tintron\t37811\t45037\t1\t+\t.\ttranscript_id \"g21534.t1\"; gene_id \"g21534\";\r\n", "1\t44942\t44944\t1\tAUGUSTUS\tintron\t37811\t45037\t1\t+\t.\ttranscript_id \"g21534.t1\"; gene_id \"g21534\";\r\n", "1\t44946\t44948\t1\tAUGUSTUS\tintron\t37811\t45037\t1\t+\t.\ttranscript_id \"g21534.t1\"; gene_id \"g21534\";\r\n", "1\t44981\t44983\t1\tAUGUSTUS\tintron\t37811\t45037\t1\t+\t.\ttranscript_id \"g21534.t1\"; gene_id \"g21534\";\r\n", "1\t44991\t44993\t1\tAUGUSTUS\tintron\t37811\t45037\t1\t+\t.\ttranscript_id \"g21534.t1\"; gene_id \"g21534\";\r\n", "\r\n", "==> Meth14_R1_001_val_1_bismark_bt2_pe._10x.bedgraph.bed-mcIntrons <==\r\n", "1\t40450\t40452\t1\tAUGUSTUS\tintron\t37811\t45037\t1\t+\t.\ttranscript_id \"g21534.t1\"; gene_id \"g21534\";\r\n", "1\t40486\t40488\t1\tAUGUSTUS\tintron\t37811\t45037\t1\t+\t.\ttranscript_id \"g21534.t1\"; gene_id \"g21534\";\r\n", "1\t40541\t40543\t1\tAUGUSTUS\tintron\t37811\t45037\t1\t+\t.\ttranscript_id \"g21534.t1\"; gene_id \"g21534\";\r\n", "1\t40552\t40554\t1\tAUGUSTUS\tintron\t37811\t45037\t1\t+\t.\ttranscript_id \"g21534.t1\"; gene_id \"g21534\";\r\n", "1\t40555\t40557\t1\tAUGUSTUS\tintron\t37811\t45037\t1\t+\t.\ttranscript_id \"g21534.t1\"; gene_id \"g21534\";\r\n", "1\t44922\t44924\t1\tAUGUSTUS\tintron\t37811\t45037\t1\t+\t.\ttranscript_id \"g21534.t1\"; gene_id \"g21534\";\r\n", "1\t44942\t44944\t1\tAUGUSTUS\tintron\t37811\t45037\t1\t+\t.\ttranscript_id \"g21534.t1\"; gene_id \"g21534\";\r\n", "1\t44946\t44948\t1\tAUGUSTUS\tintron\t37811\t45037\t1\t+\t.\ttranscript_id \"g21534.t1\"; gene_id \"g21534\";\r\n", "1\t44981\t44983\t1\tAUGUSTUS\tintron\t37811\t45037\t1\t+\t.\ttranscript_id \"g21534.t1\"; gene_id \"g21534\";\r\n", "1\t44991\t44993\t1\tAUGUSTUS\tintron\t37811\t45037\t1\t+\t.\ttranscript_id \"g21534.t1\"; gene_id \"g21534\";\r\n", "\r\n", "==> Meth15_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-Meth.bed-mcIntrons <==\r\n", "1\t101462\t101464\t1\tAUGUSTUS\tintron\t100307\t102769\t1\t-\t.\ttranscript_id \"g21538.t1\"; gene_id \"g21538\";\r\n", "1\t101535\t101537\t1\tAUGUSTUS\tintron\t100307\t102769\t1\t-\t.\ttranscript_id \"g21538.t1\"; gene_id \"g21538\";\r\n", "1\t108751\t108753\t1\tAUGUSTUS\tintron\t104815\t109637\t1\t-\t.\ttranscript_id \"g21538.t1\"; gene_id \"g21538\";\r\n", "1\t108778\t108780\t1\tAUGUSTUS\tintron\t104815\t109637\t1\t-\t.\ttranscript_id \"g21538.t1\"; gene_id \"g21538\";\r\n", "1\t108787\t108789\t1\tAUGUSTUS\tintron\t104815\t109637\t1\t-\t.\ttranscript_id \"g21538.t1\"; gene_id \"g21538\";\r\n", "1\t108803\t108805\t1\tAUGUSTUS\tintron\t104815\t109637\t1\t-\t.\ttranscript_id \"g21538.t1\"; gene_id \"g21538\";\r\n", "1\t108815\t108817\t1\tAUGUSTUS\tintron\t104815\t109637\t1\t-\t.\ttranscript_id \"g21538.t1\"; gene_id \"g21538\";\r\n", "1\t108867\t108869\t1\tAUGUSTUS\tintron\t104815\t109637\t1\t-\t.\ttranscript_id \"g21538.t1\"; gene_id \"g21538\";\r\n", "1\t108949\t108951\t1\tAUGUSTUS\tintron\t104815\t109637\t1\t-\t.\ttranscript_id \"g21538.t1\"; gene_id \"g21538\";\r\n", "1\t344358\t344360\t1\tAUGUSTUS\tintron\t341159\t344880\t1\t-\t.\ttranscript_id \"g21555.t1\"; gene_id \"g21555\";\r\n", "\r\n", "==> Meth15_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-sparseMeth.bed-mcIntrons <==\r\n", "1\t41916\t41918\t1\tAUGUSTUS\tintron\t37811\t45037\t1\t+\t.\ttranscript_id \"g21534.t1\"; gene_id \"g21534\";\r\n", "1\t42261\t42263\t1\tAUGUSTUS\tintron\t37811\t45037\t1\t+\t.\ttranscript_id \"g21534.t1\"; gene_id \"g21534\";\r\n", "1\t101503\t101505\t1\tAUGUSTUS\tintron\t100307\t102769\t1\t-\t.\ttranscript_id \"g21538.t1\"; gene_id \"g21538\";\r\n", "1\t101545\t101547\t1\tAUGUSTUS\tintron\t100307\t102769\t1\t-\t.\ttranscript_id \"g21538.t1\"; gene_id \"g21538\";\r\n", "1\t332804\t332806\t1\tAUGUSTUS\tintron\t332498\t332814\t1\t-\t.\ttranscript_id \"g21555.t1\"; gene_id \"g21555\";\r\n", "1\t336069\t336071\t1\tAUGUSTUS\tintron\t334182\t338302\t1\t-\t.\ttranscript_id \"g21555.t1\"; gene_id \"g21555\";\r\n", "1\t336217\t336219\t1\tAUGUSTUS\tintron\t334182\t338302\t1\t-\t.\ttranscript_id \"g21555.t1\"; gene_id \"g21555\";\r\n", "1\t370881\t370883\t1\tAUGUSTUS\tintron\t370723\t371754\t1\t-\t.\ttranscript_id \"g21558.t1\"; gene_id \"g21558\";\r\n", "1\t370967\t370969\t1\tAUGUSTUS\tintron\t370723\t371754\t1\t-\t.\ttranscript_id \"g21558.t1\"; gene_id \"g21558\";\r\n", "1\t527706\t527708\t1\tAUGUSTUS\tintron\t527465\t530650\t1\t-\t.\ttranscript_id \"g21573.t1\"; gene_id \"g21573\";\r\n", "\r\n", "==> Meth15_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-unMeth.bed-mcIntrons <==\r\n", "1\t40450\t40452\t1\tAUGUSTUS\tintron\t37811\t45037\t1\t+\t.\ttranscript_id \"g21534.t1\"; gene_id \"g21534\";\r\n", "1\t40486\t40488\t1\tAUGUSTUS\tintron\t37811\t45037\t1\t+\t.\ttranscript_id \"g21534.t1\"; gene_id \"g21534\";\r\n", "1\t40541\t40543\t1\tAUGUSTUS\tintron\t37811\t45037\t1\t+\t.\ttranscript_id \"g21534.t1\"; gene_id \"g21534\";\r\n", "1\t40552\t40554\t1\tAUGUSTUS\tintron\t37811\t45037\t1\t+\t.\ttranscript_id \"g21534.t1\"; gene_id \"g21534\";\r\n", "1\t40555\t40557\t1\tAUGUSTUS\tintron\t37811\t45037\t1\t+\t.\ttranscript_id \"g21534.t1\"; gene_id \"g21534\";\r\n", "1\t41832\t41834\t1\tAUGUSTUS\tintron\t37811\t45037\t1\t+\t.\ttranscript_id \"g21534.t1\"; gene_id \"g21534\";\r\n", "1\t41845\t41847\t1\tAUGUSTUS\tintron\t37811\t45037\t1\t+\t.\ttranscript_id \"g21534.t1\"; gene_id \"g21534\";\r\n", "1\t41864\t41866\t1\tAUGUSTUS\tintron\t37811\t45037\t1\t+\t.\ttranscript_id \"g21534.t1\"; gene_id \"g21534\";\r\n", "1\t41974\t41976\t1\tAUGUSTUS\tintron\t37811\t45037\t1\t+\t.\ttranscript_id \"g21534.t1\"; gene_id \"g21534\";\r\n", "1\t42117\t42119\t1\tAUGUSTUS\tintron\t37811\t45037\t1\t+\t.\ttranscript_id \"g21534.t1\"; gene_id \"g21534\";\r\n", "\r\n", "==> Meth15_R1_001_val_1_bismark_bt2_pe._10x.bedgraph.bed-mcIntrons <==\r\n", "1\t40450\t40452\t1\tAUGUSTUS\tintron\t37811\t45037\t1\t+\t.\ttranscript_id \"g21534.t1\"; gene_id \"g21534\";\r\n", "1\t40486\t40488\t1\tAUGUSTUS\tintron\t37811\t45037\t1\t+\t.\ttranscript_id \"g21534.t1\"; gene_id \"g21534\";\r\n", "1\t40541\t40543\t1\tAUGUSTUS\tintron\t37811\t45037\t1\t+\t.\ttranscript_id \"g21534.t1\"; gene_id \"g21534\";\r\n", "1\t40552\t40554\t1\tAUGUSTUS\tintron\t37811\t45037\t1\t+\t.\ttranscript_id \"g21534.t1\"; gene_id \"g21534\";\r\n", "1\t40555\t40557\t1\tAUGUSTUS\tintron\t37811\t45037\t1\t+\t.\ttranscript_id \"g21534.t1\"; gene_id \"g21534\";\r\n", "1\t41832\t41834\t1\tAUGUSTUS\tintron\t37811\t45037\t1\t+\t.\ttranscript_id \"g21534.t1\"; gene_id \"g21534\";\r\n", "1\t41845\t41847\t1\tAUGUSTUS\tintron\t37811\t45037\t1\t+\t.\ttranscript_id \"g21534.t1\"; gene_id \"g21534\";\r\n", "1\t41864\t41866\t1\tAUGUSTUS\tintron\t37811\t45037\t1\t+\t.\ttranscript_id \"g21534.t1\"; gene_id \"g21534\";\r\n", "1\t41916\t41918\t1\tAUGUSTUS\tintron\t37811\t45037\t1\t+\t.\ttranscript_id \"g21534.t1\"; gene_id \"g21534\";\r\n", "1\t41974\t41976\t1\tAUGUSTUS\tintron\t37811\t45037\t1\t+\t.\ttranscript_id \"g21534.t1\"; gene_id \"g21534\";\r\n", "\r\n", "==> Meth16_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-Meth.bed-mcIntrons <==\r\n", "1\t1536523\t1536525\t1\tAUGUSTUS\tintron\t1534875\t1541508\t1\t+\t.\ttranscript_id \"g21645.t1\"; gene_id \"g21645\";\r\n", "1\t1536643\t1536645\t1\tAUGUSTUS\tintron\t1534875\t1541508\t1\t+\t.\ttranscript_id \"g21645.t1\"; gene_id \"g21645\";\r\n", "1\t1536657\t1536659\t1\tAUGUSTUS\tintron\t1534875\t1541508\t1\t+\t.\ttranscript_id \"g21645.t1\"; gene_id \"g21645\";\r\n", "1\t1755684\t1755686\t1\tAUGUSTUS\tintron\t1754732\t1759252\t1\t-\t.\ttranscript_id \"g21659.t1\"; gene_id \"g21659\";\r\n", "1\t1958635\t1958637\t1\tAUGUSTUS\tintron\t1956809\t1960162\t1\t+\t.\ttranscript_id \"g21683.t1\"; gene_id \"g21683\";\r\n", "1\t1958667\t1958669\t1\tAUGUSTUS\tintron\t1956809\t1960162\t1\t+\t.\ttranscript_id \"g21683.t1\"; gene_id \"g21683\";\r\n", "1\t1958693\t1958695\t1\tAUGUSTUS\tintron\t1956809\t1960162\t1\t+\t.\ttranscript_id \"g21683.t1\"; gene_id \"g21683\";\r\n", "1\t1958702\t1958704\t1\tAUGUSTUS\tintron\t1956809\t1960162\t1\t+\t.\ttranscript_id \"g21683.t1\"; gene_id \"g21683\";\r\n", "1\t2264832\t2264834\t1\tAUGUSTUS\tintron\t2262613\t2265939\t1\t-\t.\ttranscript_id \"g21703.t1\"; gene_id \"g21703\";\r\n", "1\t2264871\t2264873\t1\tAUGUSTUS\tintron\t2262613\t2265939\t1\t-\t.\ttranscript_id \"g21703.t1\"; gene_id \"g21703\";\r\n", "\r\n", "==> Meth16_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-sparseMeth.bed-mcIntrons <==\r\n", "1\t1540374\t1540376\t1\tAUGUSTUS\tintron\t1534875\t1541508\t1\t+\t.\ttranscript_id \"g21645.t1\"; gene_id \"g21645\";\r\n", "4\t415651\t415653\t4\tAUGUSTUS\tintron\t403801\t415920\t0.54\t+\t.\ttranscript_id \"g22307.t1\"; gene_id \"g22307\";\r\n", "4\t415664\t415666\t4\tAUGUSTUS\tintron\t403801\t415920\t0.54\t+\t.\ttranscript_id \"g22307.t1\"; gene_id \"g22307\";\r\n", "4\t1848309\t1848311\t4\tAUGUSTUS\tintron\t1847405\t1850078\t1\t-\t.\ttranscript_id \"g22401.t1\"; gene_id \"g22401\";\r\n", "6\t1212933\t1212935\t6\tAUGUSTUS\tintron\t1212011\t1215485\t1\t-\t.\ttranscript_id \"g22753.t1\"; gene_id \"g22753\";\r\n", "6\t1212942\t1212944\t6\tAUGUSTUS\tintron\t1212011\t1215485\t1\t-\t.\ttranscript_id \"g22753.t1\"; gene_id \"g22753\";\r\n", "6\t1212960\t1212962\t6\tAUGUSTUS\tintron\t1212011\t1215485\t1\t-\t.\ttranscript_id \"g22753.t1\"; gene_id \"g22753\";\r\n", "6\t1212971\t1212973\t6\tAUGUSTUS\tintron\t1212011\t1215485\t1\t-\t.\ttranscript_id \"g22753.t1\"; gene_id \"g22753\";\r\n", "6\t2130432\t2130434\t6\tAUGUSTUS\tintron\t2130293\t2130723\t0.49\t-\t.\ttranscript_id \"g22813.t1\"; gene_id \"g22813\";\r\n", "6\t2130504\t2130506\t6\tAUGUSTUS\tintron\t2130293\t2130723\t0.49\t-\t.\ttranscript_id \"g22813.t1\"; gene_id \"g22813\";\r\n", "\r\n", "==> Meth16_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-unMeth.bed-mcIntrons <==\r\n", "1\t2311899\t2311901\t1\tAUGUSTUS\tintron\t2311616\t2312194\t1\t-\t.\ttranscript_id \"g21705.t1\"; gene_id \"g21705\";\r\n", "1\t2311908\t2311910\t1\tAUGUSTUS\tintron\t2311616\t2312194\t1\t-\t.\ttranscript_id \"g21705.t1\"; gene_id \"g21705\";\r\n", "1\t2907968\t2907970\t1\tAUGUSTUS\tintron\t2907558\t2909062\t1\t+\t.\ttranscript_id \"g21743.t1\"; gene_id \"g21743\";\r\n", "2\t773507\t773509\t2\tAUGUSTUS\tintron\t771902\t777809\t1\t+\t.\ttranscript_id \"g21893.t1\"; gene_id \"g21893\";\r\n", "4\t415666\t415668\t4\tAUGUSTUS\tintron\t403801\t415920\t0.54\t+\t.\ttranscript_id \"g22307.t1\"; gene_id \"g22307\";\r\n", "4\t1631207\t1631209\t4\tAUGUSTUS\tintron\t1629967\t1631262\t0.8\t+\t.\ttranscript_id \"g22385.t1\"; gene_id \"g22385\";\r\n", "4\t1848326\t1848328\t4\tAUGUSTUS\tintron\t1847405\t1850078\t1\t-\t.\ttranscript_id \"g22401.t1\"; gene_id \"g22401\";\r\n", "4\t1848341\t1848343\t4\tAUGUSTUS\tintron\t1847405\t1850078\t1\t-\t.\ttranscript_id \"g22401.t1\"; gene_id \"g22401\";\r\n", "4\t2291584\t2291586\t4\tAUGUSTUS\tintron\t2287749\t2295805\t0.49\t+\t.\ttranscript_id \"g22430.t1\"; gene_id \"g22430\";\r\n", "4\t2291603\t2291605\t4\tAUGUSTUS\tintron\t2287749\t2295805\t0.49\t+\t.\ttranscript_id \"g22430.t1\"; gene_id \"g22430\";\r\n", "\r\n", "==> Meth16_R1_001_val_1_bismark_bt2_pe._10x.bedgraph.bed-mcIntrons <==\r\n", "1\t1536523\t1536525\t1\tAUGUSTUS\tintron\t1534875\t1541508\t1\t+\t.\ttranscript_id \"g21645.t1\"; gene_id \"g21645\";\r\n", "1\t1536643\t1536645\t1\tAUGUSTUS\tintron\t1534875\t1541508\t1\t+\t.\ttranscript_id \"g21645.t1\"; gene_id \"g21645\";\r\n", "1\t1536657\t1536659\t1\tAUGUSTUS\tintron\t1534875\t1541508\t1\t+\t.\ttranscript_id \"g21645.t1\"; gene_id \"g21645\";\r\n", "1\t1540374\t1540376\t1\tAUGUSTUS\tintron\t1534875\t1541508\t1\t+\t.\ttranscript_id \"g21645.t1\"; gene_id \"g21645\";\r\n", "1\t1755684\t1755686\t1\tAUGUSTUS\tintron\t1754732\t1759252\t1\t-\t.\ttranscript_id \"g21659.t1\"; gene_id \"g21659\";\r\n", "1\t1958635\t1958637\t1\tAUGUSTUS\tintron\t1956809\t1960162\t1\t+\t.\ttranscript_id \"g21683.t1\"; gene_id \"g21683\";\r\n", "1\t1958667\t1958669\t1\tAUGUSTUS\tintron\t1956809\t1960162\t1\t+\t.\ttranscript_id \"g21683.t1\"; gene_id \"g21683\";\r\n", "1\t1958693\t1958695\t1\tAUGUSTUS\tintron\t1956809\t1960162\t1\t+\t.\ttranscript_id \"g21683.t1\"; gene_id \"g21683\";\r\n", "1\t1958702\t1958704\t1\tAUGUSTUS\tintron\t1956809\t1960162\t1\t+\t.\ttranscript_id \"g21683.t1\"; gene_id \"g21683\";\r\n", "1\t2264832\t2264834\t1\tAUGUSTUS\tintron\t2262613\t2265939\t1\t-\t.\ttranscript_id \"g21703.t1\"; gene_id \"g21703\";\r\n", "\r\n", "==> Meth17_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-Meth.bed-mcIntrons <==\r\n", "1\t1987244\t1987246\t1\tAUGUSTUS\tintron\t1986330\t1988617\t1\t+\t.\ttranscript_id \"g21685.t1\"; gene_id \"g21685\";\r\n", "1\t1987263\t1987265\t1\tAUGUSTUS\tintron\t1986330\t1988617\t1\t+\t.\ttranscript_id \"g21685.t1\"; gene_id \"g21685\";\r\n", "6\t2130423\t2130425\t6\tAUGUSTUS\tintron\t2130293\t2130723\t0.49\t-\t.\ttranscript_id \"g22813.t1\"; gene_id \"g22813\";\r\n", "6\t2130432\t2130434\t6\tAUGUSTUS\tintron\t2130293\t2130723\t0.49\t-\t.\ttranscript_id \"g22813.t1\"; gene_id \"g22813\";\r\n", "6\t2130436\t2130438\t6\tAUGUSTUS\tintron\t2130293\t2130723\t0.49\t-\t.\ttranscript_id \"g22813.t1\"; gene_id \"g22813\";\r\n", "6\t2130450\t2130452\t6\tAUGUSTUS\tintron\t2130293\t2130723\t0.49\t-\t.\ttranscript_id \"g22813.t1\"; gene_id \"g22813\";\r\n", "6\t2130453\t2130455\t6\tAUGUSTUS\tintron\t2130293\t2130723\t0.49\t-\t.\ttranscript_id \"g22813.t1\"; gene_id \"g22813\";\r\n", "6\t2130561\t2130563\t6\tAUGUSTUS\tintron\t2130293\t2130723\t0.49\t-\t.\ttranscript_id \"g22813.t1\"; gene_id \"g22813\";\r\n", "6\t2130654\t2130656\t6\tAUGUSTUS\tintron\t2130293\t2130723\t0.49\t-\t.\ttranscript_id \"g22813.t1\"; gene_id \"g22813\";\r\n", "6\t2130678\t2130680\t6\tAUGUSTUS\tintron\t2130293\t2130723\t0.49\t-\t.\ttranscript_id \"g22813.t1\"; gene_id \"g22813\";\r\n", "\r\n", "==> Meth17_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-sparseMeth.bed-mcIntrons <==\r\n", "4\t811595\t811597\t4\tAUGUSTUS\tintron\t810427\t812631\t1\t-\t.\ttranscript_id \"g22330.t1\"; gene_id \"g22330\";\r\n", "4\t811607\t811609\t4\tAUGUSTUS\tintron\t810427\t812631\t1\t-\t.\ttranscript_id \"g22330.t1\"; gene_id \"g22330\";\r\n", "6\t2130399\t2130401\t6\tAUGUSTUS\tintron\t2130293\t2130723\t0.49\t-\t.\ttranscript_id \"g22813.t1\"; gene_id \"g22813\";\r\n", "6\t2130495\t2130497\t6\tAUGUSTUS\tintron\t2130293\t2130723\t0.49\t-\t.\ttranscript_id \"g22813.t1\"; gene_id \"g22813\";\r\n", "6\t2130504\t2130506\t6\tAUGUSTUS\tintron\t2130293\t2130723\t0.49\t-\t.\ttranscript_id \"g22813.t1\"; gene_id \"g22813\";\r\n", "7\t1957296\t1957298\t7\tAUGUSTUS\tintron\t1954359\t1962280\t1\t-\t.\ttranscript_id \"g23037.t1\"; gene_id \"g23037\";\r\n", "7\t1957322\t1957324\t7\tAUGUSTUS\tintron\t1954359\t1962280\t1\t-\t.\ttranscript_id \"g23037.t1\"; gene_id \"g23037\";\r\n", "10\t728576\t728578\t10\tAUGUSTUS\tintron\t727738\t729377\t0.97\t+\t.\ttranscript_id \"g23341.t1\"; gene_id \"g23341\";\r\n", "10\t734228\t734230\t10\tAUGUSTUS\tintron\t733375\t736653\t0.71\t-\t.\ttranscript_id \"g23342.t1\"; gene_id \"g23342\";\r\n", "10\t734242\t734244\t10\tAUGUSTUS\tintron\t733375\t736653\t0.71\t-\t.\ttranscript_id \"g23342.t1\"; gene_id \"g23342\";\r\n", "\r\n", "==> Meth17_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-unMeth.bed-mcIntrons <==\r\n", "1\t2608371\t2608373\t1\tAUGUSTUS\tintron\t2607891\t2608908\t1\t+\t.\ttranscript_id \"g21721.t1\"; gene_id \"g21721\";\r\n", "4\t811590\t811592\t4\tAUGUSTUS\tintron\t810427\t812631\t1\t-\t.\ttranscript_id \"g22330.t1\"; gene_id \"g22330\";\r\n", "4\t2291584\t2291586\t4\tAUGUSTUS\tintron\t2287749\t2295805\t0.49\t+\t.\ttranscript_id \"g22430.t1\"; gene_id \"g22430\";\r\n", "4\t2291603\t2291605\t4\tAUGUSTUS\tintron\t2287749\t2295805\t0.49\t+\t.\ttranscript_id \"g22430.t1\"; gene_id \"g22430\";\r\n", "4\t2291633\t2291635\t4\tAUGUSTUS\tintron\t2287749\t2295805\t0.49\t+\t.\ttranscript_id \"g22430.t1\"; gene_id \"g22430\";\r\n", "4\t2291699\t2291701\t4\tAUGUSTUS\tintron\t2287749\t2295805\t0.49\t+\t.\ttranscript_id \"g22430.t1\"; gene_id \"g22430\";\r\n", "4\t2291722\t2291724\t4\tAUGUSTUS\tintron\t2287749\t2295805\t0.49\t+\t.\ttranscript_id \"g22430.t1\"; gene_id \"g22430\";\r\n", "4\t2291750\t2291752\t4\tAUGUSTUS\tintron\t2287749\t2295805\t0.49\t+\t.\ttranscript_id \"g22430.t1\"; gene_id \"g22430\";\r\n", "4\t2291757\t2291759\t4\tAUGUSTUS\tintron\t2287749\t2295805\t0.49\t+\t.\ttranscript_id \"g22430.t1\"; gene_id \"g22430\";\r\n", "4\t2291759\t2291761\t4\tAUGUSTUS\tintron\t2287749\t2295805\t0.49\t+\t.\ttranscript_id \"g22430.t1\"; gene_id \"g22430\";\r\n", "\r\n", "==> Meth17_R1_001_val_1_bismark_bt2_pe._10x.bedgraph.bed-mcIntrons <==\r\n", "1\t1987244\t1987246\t1\tAUGUSTUS\tintron\t1986330\t1988617\t1\t+\t.\ttranscript_id \"g21685.t1\"; gene_id \"g21685\";\r\n", "1\t1987263\t1987265\t1\tAUGUSTUS\tintron\t1986330\t1988617\t1\t+\t.\ttranscript_id \"g21685.t1\"; gene_id \"g21685\";\r\n", "1\t2608371\t2608373\t1\tAUGUSTUS\tintron\t2607891\t2608908\t1\t+\t.\ttranscript_id \"g21721.t1\"; gene_id \"g21721\";\r\n", "4\t811590\t811592\t4\tAUGUSTUS\tintron\t810427\t812631\t1\t-\t.\ttranscript_id \"g22330.t1\"; gene_id \"g22330\";\r\n", "4\t811595\t811597\t4\tAUGUSTUS\tintron\t810427\t812631\t1\t-\t.\ttranscript_id \"g22330.t1\"; gene_id \"g22330\";\r\n", "4\t811607\t811609\t4\tAUGUSTUS\tintron\t810427\t812631\t1\t-\t.\ttranscript_id \"g22330.t1\"; gene_id \"g22330\";\r\n", "4\t2291584\t2291586\t4\tAUGUSTUS\tintron\t2287749\t2295805\t0.49\t+\t.\ttranscript_id \"g22430.t1\"; gene_id \"g22430\";\r\n", "4\t2291603\t2291605\t4\tAUGUSTUS\tintron\t2287749\t2295805\t0.49\t+\t.\ttranscript_id \"g22430.t1\"; gene_id \"g22430\";\r\n", "4\t2291633\t2291635\t4\tAUGUSTUS\tintron\t2287749\t2295805\t0.49\t+\t.\ttranscript_id \"g22430.t1\"; gene_id \"g22430\";\r\n", "4\t2291699\t2291701\t4\tAUGUSTUS\tintron\t2287749\t2295805\t0.49\t+\t.\ttranscript_id \"g22430.t1\"; gene_id \"g22430\";\r\n", "\r\n", "==> Meth18_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-Meth.bed-mcIntrons <==\r\n", "6\t2130678\t2130680\t6\tAUGUSTUS\tintron\t2130293\t2130723\t0.49\t-\t.\ttranscript_id \"g22813.t1\"; gene_id \"g22813\";\r\n", "6\t2130702\t2130704\t6\tAUGUSTUS\tintron\t2130293\t2130723\t0.49\t-\t.\ttranscript_id \"g22813.t1\"; gene_id \"g22813\";\r\n", "10\t733382\t733384\t10\tAUGUSTUS\tintron\t733375\t736653\t0.71\t-\t.\ttranscript_id \"g23342.t1\"; gene_id \"g23342\";\r\n", "11\t70372\t70374\t11\tAUGUSTUS\tintron\t69842\t73769\t1\t+\t.\ttranscript_id \"g23521.t1\"; gene_id \"g23521\";\r\n", "11\t70379\t70381\t11\tAUGUSTUS\tintron\t69842\t73769\t1\t+\t.\ttranscript_id \"g23521.t1\"; gene_id \"g23521\";\r\n", "11\t70383\t70385\t11\tAUGUSTUS\tintron\t69842\t73769\t1\t+\t.\ttranscript_id \"g23521.t1\"; gene_id \"g23521\";\r\n", "11\t70386\t70388\t11\tAUGUSTUS\tintron\t69842\t73769\t1\t+\t.\ttranscript_id \"g23521.t1\"; gene_id \"g23521\";\r\n", "11\t70395\t70397\t11\tAUGUSTUS\tintron\t69842\t73769\t1\t+\t.\ttranscript_id \"g23521.t1\"; gene_id \"g23521\";\r\n", "11\t70734\t70736\t11\tAUGUSTUS\tintron\t69842\t73769\t1\t+\t.\ttranscript_id \"g23521.t1\"; gene_id \"g23521\";\r\n", "11\t70754\t70756\t11\tAUGUSTUS\tintron\t69842\t73769\t1\t+\t.\ttranscript_id \"g23521.t1\"; gene_id \"g23521\";\r\n", "\r\n", "==> Meth18_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-sparseMeth.bed-mcIntrons <==\r\n", "7\t86796\t86798\t7\tAUGUSTUS\tintron\t85134\t88777\t0.8\t+\t.\ttranscript_id \"g22864.t1\"; gene_id \"g22864\";\r\n", "21\t1326374\t1326376\t21\tAUGUSTUS\tintron\t1320432\t1328776\t0.51\t-\t.\ttranscript_id \"g25222.t1\"; gene_id \"g25222\";\r\n", "24\t1663542\t1663544\t24\tAUGUSTUS\tintron\t1659135\t1673738\t1\t-\t.\ttranscript_id \"g25540.t1\"; gene_id \"g25540\";\r\n", "24\t1663878\t1663880\t24\tAUGUSTUS\tintron\t1659135\t1673738\t1\t-\t.\ttranscript_id \"g25540.t1\"; gene_id \"g25540\";\r\n", "24\t1670426\t1670428\t24\tAUGUSTUS\tintron\t1659135\t1673738\t1\t-\t.\ttranscript_id \"g25540.t1\"; gene_id \"g25540\";\r\n", "26\t243418\t243420\t26\tAUGUSTUS\tintron\t236599\t244175\t1\t-\t.\ttranscript_id \"g25709.t1\"; gene_id \"g25709\";\r\n", "27\t1831897\t1831899\t27\tAUGUSTUS\tintron\t1830510\t1836099\t0.51\t-\t.\ttranscript_id \"g26013.t1\"; gene_id \"g26013\";\r\n", "27\t1832231\t1832233\t27\tAUGUSTUS\tintron\t1830510\t1836099\t0.51\t-\t.\ttranscript_id \"g26013.t1\"; gene_id \"g26013\";\r\n", "27\t1832239\t1832241\t27\tAUGUSTUS\tintron\t1830510\t1836099\t0.51\t-\t.\ttranscript_id \"g26013.t1\"; gene_id \"g26013\";\r\n", "27\t1832250\t1832252\t27\tAUGUSTUS\tintron\t1830510\t1836099\t0.51\t-\t.\ttranscript_id \"g26013.t1\"; gene_id \"g26013\";\r\n", "\r\n", "==> Meth18_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-unMeth.bed-mcIntrons <==\r\n", "4\t2291584\t2291586\t4\tAUGUSTUS\tintron\t2287749\t2295805\t0.49\t+\t.\ttranscript_id \"g22430.t1\"; gene_id \"g22430\";\r\n", "4\t2291603\t2291605\t4\tAUGUSTUS\tintron\t2287749\t2295805\t0.49\t+\t.\ttranscript_id \"g22430.t1\"; gene_id \"g22430\";\r\n", "4\t2291633\t2291635\t4\tAUGUSTUS\tintron\t2287749\t2295805\t0.49\t+\t.\ttranscript_id \"g22430.t1\"; gene_id \"g22430\";\r\n", "4\t2291699\t2291701\t4\tAUGUSTUS\tintron\t2287749\t2295805\t0.49\t+\t.\ttranscript_id \"g22430.t1\"; gene_id \"g22430\";\r\n", "4\t2291722\t2291724\t4\tAUGUSTUS\tintron\t2287749\t2295805\t0.49\t+\t.\ttranscript_id \"g22430.t1\"; gene_id \"g22430\";\r\n", "4\t2291750\t2291752\t4\tAUGUSTUS\tintron\t2287749\t2295805\t0.49\t+\t.\ttranscript_id \"g22430.t1\"; gene_id \"g22430\";\r\n", "4\t2291757\t2291759\t4\tAUGUSTUS\tintron\t2287749\t2295805\t0.49\t+\t.\ttranscript_id \"g22430.t1\"; gene_id \"g22430\";\r\n", "4\t2291759\t2291761\t4\tAUGUSTUS\tintron\t2287749\t2295805\t0.49\t+\t.\ttranscript_id \"g22430.t1\"; gene_id \"g22430\";\r\n", "6\t2130714\t2130716\t6\tAUGUSTUS\tintron\t2130293\t2130723\t0.49\t-\t.\ttranscript_id \"g22813.t1\"; gene_id \"g22813\";\r\n", "14\t1606596\t1606598\t14\tAUGUSTUS\tintron\t1604547\t1606971\t1\t-\t.\ttranscript_id \"g24037.t1\"; gene_id \"g24037\";\r\n", "\r\n", "==> Meth18_R1_001_val_1_bismark_bt2_pe._10x.bedgraph.bed-mcIntrons <==\r\n", "4\t2291584\t2291586\t4\tAUGUSTUS\tintron\t2287749\t2295805\t0.49\t+\t.\ttranscript_id \"g22430.t1\"; gene_id \"g22430\";\r\n", "4\t2291603\t2291605\t4\tAUGUSTUS\tintron\t2287749\t2295805\t0.49\t+\t.\ttranscript_id \"g22430.t1\"; gene_id \"g22430\";\r\n", "4\t2291633\t2291635\t4\tAUGUSTUS\tintron\t2287749\t2295805\t0.49\t+\t.\ttranscript_id \"g22430.t1\"; gene_id \"g22430\";\r\n", "4\t2291699\t2291701\t4\tAUGUSTUS\tintron\t2287749\t2295805\t0.49\t+\t.\ttranscript_id \"g22430.t1\"; gene_id \"g22430\";\r\n", "4\t2291722\t2291724\t4\tAUGUSTUS\tintron\t2287749\t2295805\t0.49\t+\t.\ttranscript_id \"g22430.t1\"; gene_id \"g22430\";\r\n", "4\t2291750\t2291752\t4\tAUGUSTUS\tintron\t2287749\t2295805\t0.49\t+\t.\ttranscript_id \"g22430.t1\"; gene_id \"g22430\";\r\n", "4\t2291757\t2291759\t4\tAUGUSTUS\tintron\t2287749\t2295805\t0.49\t+\t.\ttranscript_id \"g22430.t1\"; gene_id \"g22430\";\r\n", "4\t2291759\t2291761\t4\tAUGUSTUS\tintron\t2287749\t2295805\t0.49\t+\t.\ttranscript_id \"g22430.t1\"; gene_id \"g22430\";\r\n", "6\t2130678\t2130680\t6\tAUGUSTUS\tintron\t2130293\t2130723\t0.49\t-\t.\ttranscript_id \"g22813.t1\"; gene_id \"g22813\";\r\n", "6\t2130702\t2130704\t6\tAUGUSTUS\tintron\t2130293\t2130723\t0.49\t-\t.\ttranscript_id \"g22813.t1\"; gene_id \"g22813\";\r\n" ] } ], "source": [ "#Check output\n", "!head *mcIntrons" ] }, { "cell_type": "code", "execution_count": 57, "metadata": { "scrolled": true }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ " 11106 Meth10_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-Meth.bed-mcIntrons\n", " 8003 Meth10_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-sparseMeth.bed-mcIntrons\n", " 77481 Meth10_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-unMeth.bed-mcIntrons\n", " 96590 Meth10_R1_001_val_1_bismark_bt2_pe._10x.bedgraph.bed-mcIntrons\n", " 15088 Meth11_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-Meth.bed-mcIntrons\n", " 7793 Meth11_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-sparseMeth.bed-mcIntrons\n", " 76641 Meth11_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-unMeth.bed-mcIntrons\n", " 99522 Meth11_R1_001_val_1_bismark_bt2_pe._10x.bedgraph.bed-mcIntrons\n", " 57278 Meth12_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-Meth.bed-mcIntrons\n", " 27323 Meth12_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-sparseMeth.bed-mcIntrons\n", " 340957 Meth12_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-unMeth.bed-mcIntrons\n", " 425558 Meth12_R1_001_val_1_bismark_bt2_pe._10x.bedgraph.bed-mcIntrons\n", " 85069 Meth13_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-Meth.bed-mcIntrons\n", " 35795 Meth13_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-sparseMeth.bed-mcIntrons\n", " 678120 Meth13_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-unMeth.bed-mcIntrons\n", " 798984 Meth13_R1_001_val_1_bismark_bt2_pe._10x.bedgraph.bed-mcIntrons\n", " 57748 Meth14_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-Meth.bed-mcIntrons\n", " 30463 Meth14_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-sparseMeth.bed-mcIntrons\n", " 541145 Meth14_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-unMeth.bed-mcIntrons\n", " 629356 Meth14_R1_001_val_1_bismark_bt2_pe._10x.bedgraph.bed-mcIntrons\n", " 75177 Meth15_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-Meth.bed-mcIntrons\n", " 41135 Meth15_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-sparseMeth.bed-mcIntrons\n", " 662180 Meth15_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-unMeth.bed-mcIntrons\n", " 778492 Meth15_R1_001_val_1_bismark_bt2_pe._10x.bedgraph.bed-mcIntrons\n", " 4347 Meth16_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-Meth.bed-mcIntrons\n", " 595 Meth16_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-sparseMeth.bed-mcIntrons\n", " 1899 Meth16_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-unMeth.bed-mcIntrons\n", " 6841 Meth16_R1_001_val_1_bismark_bt2_pe._10x.bedgraph.bed-mcIntrons\n", " 1618 Meth17_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-Meth.bed-mcIntrons\n", " 291 Meth17_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-sparseMeth.bed-mcIntrons\n", " 915 Meth17_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-unMeth.bed-mcIntrons\n", " 2824 Meth17_R1_001_val_1_bismark_bt2_pe._10x.bedgraph.bed-mcIntrons\n", " 1270 Meth18_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-Meth.bed-mcIntrons\n", " 73 Meth18_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-sparseMeth.bed-mcIntrons\n", " 657 Meth18_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-unMeth.bed-mcIntrons\n", " 2000 Meth18_R1_001_val_1_bismark_bt2_pe._10x.bedgraph.bed-mcIntrons\n", " 5680334 total\n" ] } ], "source": [ "#Count number of overlaps\n", "!wc -l *mcIntrons" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "#### 4e. Intergenic" ] }, { "cell_type": "code", "execution_count": 59, "metadata": { "collapsed": true }, "outputs": [], "source": [ "%%bash \n", "\n", "for f in *bed\n", "do\n", " /usr/local/bin/intersectBed \\\n", " -v \\\n", " -a ${f} \\\n", " -b ../../../genome-feature-files/Mcap.GFFannotation.gene.gff \\\n", " > ${f}-mcIntergenic\n", "done" ] }, { "cell_type": "code", "execution_count": 62, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "==> Meth10_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-Meth.bed-mcIntergenic <==\r\n", "1\t448144\t448146\r\n", "1\t1452018\t1452020\r\n", "1\t1493410\t1493412\r\n", "1\t1501753\t1501755\r\n", "1\t1615321\t1615323\r\n", "1\t1745064\t1745066\r\n", "1\t1745079\t1745081\r\n", "1\t1745124\t1745126\r\n", "1\t1745150\t1745152\r\n", "1\t1745187\t1745189\r\n", "\r\n", "==> Meth10_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-sparseMeth.bed-mcIntergenic <==\r\n", "1\t405936\t405938\r\n", "1\t460307\t460309\r\n", "1\t463857\t463859\r\n", "1\t601991\t601993\r\n", "1\t602010\t602012\r\n", "1\t602012\t602014\r\n", "1\t604742\t604744\r\n", "1\t636890\t636892\r\n", "1\t664012\t664014\r\n", "1\t664080\t664082\r\n", "\r\n", "==> Meth10_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-unMeth.bed-mcIntergenic <==\r\n", "1\t208521\t208523\r\n", "1\t208524\t208526\r\n", "1\t212911\t212913\r\n", "1\t213160\t213162\r\n", "1\t213207\t213209\r\n", "1\t213247\t213249\r\n", "1\t213252\t213254\r\n", "1\t217269\t217271\r\n", "1\t217349\t217351\r\n", "1\t241116\t241118\r\n", "\r\n", "==> Meth10_R1_001_val_1_bismark_bt2_pe._10x.bedgraph.bed-mcIntergenic <==\r\n", "1\t208521\t208523\r\n", "1\t208524\t208526\r\n", "1\t212911\t212913\r\n", "1\t213160\t213162\r\n", "1\t213207\t213209\r\n", "1\t213247\t213249\r\n", "1\t213252\t213254\r\n", "1\t217269\t217271\r\n", "1\t217349\t217351\r\n", "1\t241116\t241118\r\n", "\r\n", "==> Meth11_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-Meth.bed-mcIntergenic <==\r\n", "1\t448144\t448146\r\n", "1\t450663\t450665\r\n", "1\t450675\t450677\r\n", "1\t450703\t450705\r\n", "1\t1454043\t1454045\r\n", "1\t1935424\t1935426\r\n", "1\t1935447\t1935449\r\n", "1\t1935451\t1935453\r\n", "1\t1935469\t1935471\r\n", "1\t1935472\t1935474\r\n", "\r", "\r\n", "==> Meth11_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-sparseMeth.bed-mcIntergenic <==\r\n", "1\t219905\t219907\r\n", "1\t230777\t230779\r\n", "1\t272290\t272292\r\n", "1\t411793\t411795\r\n", "1\t425364\t425366\r\n", "1\t460884\t460886\r\n", "1\t460920\t460922\r\n", "1\t460947\t460949\r\n", "1\t460953\t460955\r\n", "1\t461445\t461447\r\n", "\r\n", "==> Meth11_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-unMeth.bed-mcIntergenic <==\r\n", "1\t6453\t6455\r\n", "1\t6484\t6486\r\n", "1\t221750\t221752\r\n", "1\t223373\t223375\r\n", "1\t229852\t229854\r\n", "1\t230363\t230365\r\n", "1\t230742\t230744\r\n", "1\t230854\t230856\r\n", "1\t232150\t232152\r\n", "1\t233751\t233753\r\n", "\r\n", "==> Meth11_R1_001_val_1_bismark_bt2_pe._10x.bedgraph.bed-mcIntergenic <==\r\n", "1\t6453\t6455\r\n", "1\t6484\t6486\r\n", "1\t219905\t219907\r\n", "1\t221750\t221752\r\n", "1\t223373\t223375\r\n", "1\t229852\t229854\r\n", "1\t230363\t230365\r\n", "1\t230742\t230744\r\n", "1\t230777\t230779\r\n", "1\t230854\t230856\r\n", "\r\n", "==> Meth12_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-Meth.bed-mcIntergenic <==\r\n", "1\t450663\t450665\r\n", "1\t450675\t450677\r\n", "1\t450703\t450705\r\n", "1\t450730\t450732\r\n", "1\t451429\t451431\r\n", "1\t789333\t789335\r\n", "1\t1070688\t1070690\r\n", "1\t1070701\t1070703\r\n", "1\t1340904\t1340906\r\n", "1\t1340916\t1340918\r\n", "\r\n", "==> Meth12_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-sparseMeth.bed-mcIntergenic <==\r\n", "1\t205989\t205991\r\n", "1\t216074\t216076\r\n", "1\t243227\t243229\r\n", "1\t273081\t273083\r\n", "1\t380405\t380407\r\n", "1\t380486\t380488\r\n", "1\t382279\t382281\r\n", "1\t382287\t382289\r\n", "1\t382291\t382293\r\n", "1\t382305\t382307\r\n", "\r\n", "==> Meth12_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-unMeth.bed-mcIntergenic <==\r\n", "1\t5243\t5245\r\n", "1\t5296\t5298\r\n", "1\t5332\t5334\r\n", "1\t5343\t5345\r\n", "1\t5368\t5370\r\n", "1\t5665\t5667\r\n", "1\t5737\t5739\r\n", "1\t5749\t5751\r\n", "1\t5751\t5753\r\n", "1\t6320\t6322\r\n", "\r\n", "==> Meth12_R1_001_val_1_bismark_bt2_pe._10x.bedgraph.bed-mcIntergenic <==\r\n", "1\t5243\t5245\r\n", "1\t5296\t5298\r\n", "1\t5332\t5334\r\n", "1\t5343\t5345\r\n", "1\t5368\t5370\r\n", "1\t5665\t5667\r\n", "1\t5737\t5739\r\n", "1\t5749\t5751\r\n", "1\t5751\t5753\r\n", "1\t6320\t6322\r\n", "\r\n", "==> Meth13_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-Meth.bed-mcIntergenic <==\r\n", "1\t147722\t147724\r\n", "1\t147732\t147734\r\n", "1\t147767\t147769\r\n", "1\t147785\t147787\r\n", "1\t147794\t147796\r\n", "1\t147806\t147808\r\n", "1\t274922\t274924\r\n", "1\t274940\t274942\r\n", "1\t275004\t275006\r\n", "1\t275006\t275008\r\n", "\r\n", "==> Meth13_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-sparseMeth.bed-mcIntergenic <==\r\n", "1\t15092\t15094\r\n", "1\t21739\t21741\r\n", "1\t34139\t34141\r\n", "1\t169847\t169849\r\n", "1\t198078\t198080\r\n", "1\t227400\t227402\r\n", "1\t227407\t227409\r\n", "1\t227416\t227418\r\n", "1\t241592\t241594\r\n", "1\t255850\t255852\r\n", "\r\n", "==> Meth13_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-unMeth.bed-mcIntergenic <==\r\n", "1\t3493\t3495\r\n", "1\t3518\t3520\r\n", "1\t3727\t3729\r\n", "1\t3752\t3754\r\n", "1\t3757\t3759\r\n", "1\t3770\t3772\r\n", "1\t11979\t11981\r\n", "1\t11985\t11987\r\n", "1\t11994\t11996\r\n", "1\t12043\t12045\r\n", "\r\n", "==> Meth13_R1_001_val_1_bismark_bt2_pe._10x.bedgraph.bed-mcIntergenic <==\r\n", "1\t3493\t3495\r\n", "1\t3518\t3520\r\n", "1\t3727\t3729\r\n", "1\t3752\t3754\r\n", "1\t3757\t3759\r\n", "1\t3770\t3772\r\n", "1\t11979\t11981\r\n", "1\t11985\t11987\r\n", "1\t11994\t11996\r\n", "1\t12043\t12045\r\n", "\r\n", "==> Meth14_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-Meth.bed-mcIntergenic <==\r\n", "1\t317029\t317031\r\n", "1\t455318\t455320\r\n", "1\t616272\t616274\r\n", "1\t926227\t926229\r\n", "1\t926244\t926246\r\n", "1\t926302\t926304\r\n", "1\t926311\t926313\r\n", "1\t926371\t926373\r\n", "1\t926384\t926386\r\n", "1\t1137788\t1137790\r\n", "\r\n", "==> Meth14_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-sparseMeth.bed-mcIntergenic <==\r\n", "1\t166013\t166015\r\n", "1\t227400\t227402\r\n", "1\t246955\t246957\r\n", "1\t248898\t248900\r\n", "1\t305489\t305491\r\n", "1\t309954\t309956\r\n", "1\t314160\t314162\r\n", "1\t314207\t314209\r\n", "1\t314212\t314214\r\n", "1\t320382\t320384\r\n", "\r\n", "==> Meth14_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-unMeth.bed-mcIntergenic <==\r\n", "1\t3727\t3729\r\n", "1\t3752\t3754\r\n", "1\t3757\t3759\r\n", "1\t3770\t3772\r\n", "1\t12314\t12316\r\n", "1\t12331\t12333\r\n", "1\t12350\t12352\r\n", "1\t12352\t12354\r\n", "1\t12364\t12366\r\n", "1\t12383\t12385\r\n", "\r\n", "==> Meth14_R1_001_val_1_bismark_bt2_pe._10x.bedgraph.bed-mcIntergenic <==\r\n", "1\t3727\t3729\r\n", "1\t3752\t3754\r\n", "1\t3757\t3759\r\n", "1\t3770\t3772\r\n", "1\t12314\t12316\r\n", "1\t12331\t12333\r\n", "1\t12350\t12352\r\n", "1\t12352\t12354\r\n", "1\t12364\t12366\r\n", "1\t12383\t12385\r\n", "\r\n", "==> Meth15_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-Meth.bed-mcIntergenic <==\r\n", "1\t130507\t130509\r\n", "1\t317029\t317031\r\n", "1\t615972\t615974\r\n", "1\t616115\t616117\r\n", "1\t616146\t616148\r\n", "1\t926227\t926229\r\n", "1\t926244\t926246\r\n", "1\t926302\t926304\r\n", "1\t926311\t926313\r\n", "1\t926371\t926373\r\n", "\r\n", "==> Meth15_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-sparseMeth.bed-mcIntergenic <==\r\n", "1\t169847\t169849\r\n", "1\t169891\t169893\r\n", "1\t169927\t169929\r\n", "1\t169936\t169938\r\n", "1\t170062\t170064\r\n", "1\t170097\t170099\r\n", "1\t170127\t170129\r\n", "1\t170144\t170146\r\n", "1\t170176\t170178\r\n", "1\t170211\t170213\r\n", "\r\n", "==> Meth15_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-unMeth.bed-mcIntergenic <==\r\n", "1\t3493\t3495\r\n", "1\t3518\t3520\r\n", "1\t3727\t3729\r\n", "1\t3752\t3754\r\n", "1\t3757\t3759\r\n", "1\t3770\t3772\r\n", "1\t29753\t29755\r\n", "1\t29821\t29823\r\n", "1\t32243\t32245\r\n", "1\t32283\t32285\r\n", "\r\n", "==> Meth15_R1_001_val_1_bismark_bt2_pe._10x.bedgraph.bed-mcIntergenic <==\r\n", "1\t3493\t3495\r\n", "1\t3518\t3520\r\n", "1\t3727\t3729\r\n", "1\t3752\t3754\r\n", "1\t3757\t3759\r\n", "1\t3770\t3772\r\n", "1\t29753\t29755\r\n", "1\t29821\t29823\r\n", "1\t32243\t32245\r\n", "1\t32283\t32285\r\n", "\r\n", "==> Meth16_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-Meth.bed-mcIntergenic <==\r\n", "1\t2069354\t2069356\r\n", "1\t2069356\t2069358\r\n", "1\t2069362\t2069364\r\n", "1\t2069365\t2069367\r\n", "1\t2069369\t2069371\r\n", "1\t2069371\t2069373\r\n", "1\t2069381\t2069383\r\n", "1\t2069383\t2069385\r\n", "2\t81840\t81842\r\n", "2\t81845\t81847\r\n", "\r\n", "==> Meth16_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-sparseMeth.bed-mcIntergenic <==\r\n", "2\t330579\t330581\r\n", "2\t1463459\t1463461\r\n", "2\t1463493\t1463495\r\n", "2\t1463513\t1463515\r\n", "2\t1463518\t1463520\r\n", "2\t1463525\t1463527\r\n", "2\t1463591\t1463593\r\n", "2\t1753305\t1753307\r\n", "2\t1922072\t1922074\r\n", "2\t1976658\t1976660\r\n", "\r\n", "==> Meth16_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-unMeth.bed-mcIntergenic <==\r\n", "1\t2111902\t2111904\r\n", "1\t2111995\t2111997\r\n", "1\t2112003\t2112005\r\n", "1\t2112031\t2112033\r\n", "1\t2112033\t2112035\r\n", "1\t2112044\t2112046\r\n", "1\t2420948\t2420950\r\n", "1\t2420953\t2420955\r\n", "1\t2420957\t2420959\r\n", "1\t2420962\t2420964\r\n", "\r\n", "==> Meth16_R1_001_val_1_bismark_bt2_pe._10x.bedgraph.bed-mcIntergenic <==\r\n", "1\t2069354\t2069356\r\n", "1\t2069356\t2069358\r\n", "1\t2069362\t2069364\r\n", "1\t2069365\t2069367\r\n", "1\t2069369\t2069371\r\n", "1\t2069371\t2069373\r\n", "1\t2069381\t2069383\r\n", "1\t2069383\t2069385\r\n", "1\t2111902\t2111904\r\n", "1\t2111995\t2111997\r\n", "\r\n", "==> Meth17_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-Meth.bed-mcIntergenic <==\r\n", "2\t2679583\t2679585\r\n", "2\t2679593\t2679595\r\n", "2\t2680034\t2680036\r\n", "2\t2881267\t2881269\r\n", "2\t2902772\t2902774\r\n", "2\t3225309\t3225311\r\n", "2\t3225315\t3225317\r\n", "2\t3225328\t3225330\r\n", "2\t3225337\t3225339\r\n", "2\t3225350\t3225352\r\n", "\r\n", "==> Meth17_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-sparseMeth.bed-mcIntergenic <==\r\n", "2\t1753367\t1753369\r\n", "2\t2676061\t2676063\r\n", "2\t2680138\t2680140\r\n", "2\t2680144\t2680146\r\n", "2\t2750686\t2750688\r\n", "2\t2750688\t2750690\r\n", "2\t3225324\t3225326\r\n", "2\t3234908\t3234910\r\n", "4\t2280739\t2280741\r\n", "4\t2762159\t2762161\r\n", "\r\n", "==> Meth17_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-unMeth.bed-mcIntergenic <==\r\n", "1\t2528819\t2528821\r\n", "1\t2528872\t2528874\r\n", "1\t2528900\t2528902\r\n", "1\t2529124\t2529126\r\n", "1\t3052318\t3052320\r\n", "1\t3052336\t3052338\r\n", "2\t1780979\t1780981\r\n", "2\t1781016\t1781018\r\n", "2\t1804233\t1804235\r\n", "2\t1804297\t1804299\r\n", "\r\n", "==> Meth17_R1_001_val_1_bismark_bt2_pe._10x.bedgraph.bed-mcIntergenic <==\r\n", "1\t2528819\t2528821\r\n", "1\t2528872\t2528874\r\n", "1\t2528900\t2528902\r\n", "1\t2529124\t2529126\r\n", "1\t3052318\t3052320\r\n", "1\t3052336\t3052338\r\n", "2\t1753367\t1753369\r\n", "2\t1780979\t1780981\r\n", "2\t1781016\t1781018\r\n", "2\t1804233\t1804235\r\n", "\r\n", "==> Meth18_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-Meth.bed-mcIntergenic <==\r\n", "2\t330308\t330310\r\n", "2\t330327\t330329\r\n", "2\t330330\t330332\r\n", "2\t330347\t330349\r\n", "2\t330364\t330366\r\n", "2\t330370\t330372\r\n", "2\t330517\t330519\r\n", "2\t330579\t330581\r\n", "2\t330608\t330610\r\n", "2\t330617\t330619\r\n", "\r\n", "==> Meth18_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-sparseMeth.bed-mcIntergenic <==\r\n", "1\t3250296\t3250298\r\n", "4\t2280510\t2280512\r\n", "4\t2282559\t2282561\r\n", "4\t2282561\t2282563\r\n", "4\t2761930\t2761932\r\n", "4\t2761958\t2761960\r\n", "5\t1381856\t1381858\r\n", "6\t2158174\t2158176\r\n", "7\t1092583\t1092585\r\n", "10\t731737\t731739\r\n", "\r\n", "==> Meth18_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-unMeth.bed-mcIntergenic <==\r\n", "1\t1620404\t1620406\r\n", "1\t2528872\t2528874\r\n", "1\t2528900\t2528902\r\n", "1\t2529124\t2529126\r\n", "1\t3161844\t3161846\r\n", "1\t3161850\t3161852\r\n", "1\t3161856\t3161858\r\n", "1\t3161865\t3161867\r\n", "1\t3161905\t3161907\r\n", "1\t3248218\t3248220\r\n", "\r\n", "==> Meth18_R1_001_val_1_bismark_bt2_pe._10x.bedgraph.bed-mcIntergenic <==\r\n", "1\t1620404\t1620406\r\n", "1\t2528872\t2528874\r\n", "1\t2528900\t2528902\r\n", "1\t2529124\t2529126\r\n", "1\t3161844\t3161846\r\n", "1\t3161850\t3161852\r\n", "1\t3161856\t3161858\r\n", "1\t3161865\t3161867\r\n", "1\t3161905\t3161907\r\n", "1\t3248218\t3248220\r\n" ] } ], "source": [ "#Check output\n", "!head *mcIntergenic" ] }, { "cell_type": "code", "execution_count": 63, "metadata": { "scrolled": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ " 18481 Meth10_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-Meth.bed-mcIntergenic\n", " 27758 Meth10_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-sparseMeth.bed-mcIntergenic\n", " 264552 Meth10_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-unMeth.bed-mcIntergenic\n", " 310791 Meth10_R1_001_val_1_bismark_bt2_pe._10x.bedgraph.bed-mcIntergenic\n", " 26477 Meth11_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-Meth.bed-mcIntergenic\n", " 27417 Meth11_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-sparseMeth.bed-mcIntergenic\n", " 259116 Meth11_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-unMeth.bed-mcIntergenic\n", " 313010 Meth11_R1_001_val_1_bismark_bt2_pe._10x.bedgraph.bed-mcIntergenic\n", " 90341 Meth12_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-Meth.bed-mcIntergenic\n", " 83053 Meth12_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-sparseMeth.bed-mcIntergenic\n", " 949351 Meth12_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-unMeth.bed-mcIntergenic\n", " 1122745 Meth12_R1_001_val_1_bismark_bt2_pe._10x.bedgraph.bed-mcIntergenic\n", " 105044 Meth13_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-Meth.bed-mcIntergenic\n", " 83039 Meth13_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-sparseMeth.bed-mcIntergenic\n", " 1769026 Meth13_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-unMeth.bed-mcIntergenic\n", " 1957109 Meth13_R1_001_val_1_bismark_bt2_pe._10x.bedgraph.bed-mcIntergenic\n", " 69491 Meth14_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-Meth.bed-mcIntergenic\n", " 68273 Meth14_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-sparseMeth.bed-mcIntergenic\n", " 1391975 Meth14_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-unMeth.bed-mcIntergenic\n", " 1529739 Meth14_R1_001_val_1_bismark_bt2_pe._10x.bedgraph.bed-mcIntergenic\n", " 86666 Meth15_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-Meth.bed-mcIntergenic\n", " 92547 Meth15_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-sparseMeth.bed-mcIntergenic\n", " 1730212 Meth15_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-unMeth.bed-mcIntergenic\n", " 1909425 Meth15_R1_001_val_1_bismark_bt2_pe._10x.bedgraph.bed-mcIntergenic\n", " 9778 Meth16_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-Meth.bed-mcIntergenic\n", " 4068 Meth16_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-sparseMeth.bed-mcIntergenic\n", " 18746 Meth16_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-unMeth.bed-mcIntergenic\n", " 32592 Meth16_R1_001_val_1_bismark_bt2_pe._10x.bedgraph.bed-mcIntergenic\n", " 3707 Meth17_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-Meth.bed-mcIntergenic\n", " 1771 Meth17_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-sparseMeth.bed-mcIntergenic\n", " 11192 Meth17_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-unMeth.bed-mcIntergenic\n", " 16670 Meth17_R1_001_val_1_bismark_bt2_pe._10x.bedgraph.bed-mcIntergenic\n", " 2819 Meth18_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-Meth.bed-mcIntergenic\n", " 1268 Meth18_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-sparseMeth.bed-mcIntergenic\n", " 7453 Meth18_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-unMeth.bed-mcIntergenic\n", " 11540 Meth18_R1_001_val_1_bismark_bt2_pe._10x.bedgraph.bed-mcIntergenic\n", " 14407242 total\n" ] } ], "source": [ "#Count number of overlaps\n", "!wc -l *mcIntergenic" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "#### Summary" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "##### Overlaps with Genes\n", "\n", "| **Sample** \t| **Method** \t| **CpG with Data** \t| **Methylated CpG** \t| **Sparsely Methylated CpG** \t| **Unmethylated CpG** \t|\n", "|------------\t|------------\t|-------------------\t|--------------------\t|-----------------------------\t|----------------------\t|\n", "| 10 \t| WGBS \t| 160102 \t| 17007 (10.6%) \t| 15647 (9.8%) \t| 127448 (79.6%) \t|\n", "| 11 \t| WGBS \t| 166510 \t| 23163 (13.9%) \t| 15042 (9.0%) \t| 128305 (77.1%) \t|\n", "| 12 \t| WGBS \t| 634252 \t| 82744 (13.0%) \t| 44107 (7.0%) \t| 507401 (80.0%) \t|\n", "| 13 \t| RRBS \t| 988858 \t| 99753 (10.1%) \t| 46167 (4.7%) \t| 842938 (85.2%) \t|\n", "| 14 \t| RRBS \t| 780718 \t| 67014 (8.6%) \t| 39102 (5.0%) \t| 674602 (86.4%) \t|\n", "| 15 \t| RRBS \t| 964930 \t| 86291 (8.9%) \t| 53429 (5.5%) \t| 825210 (85.5%) \t|\n", "| 16 \t| MBD-BSSeq \t| 11499 \t| 6390 (55.6%) \t| 1215 (10.6%) \t| 3894 (33.9%) \t|\n", "| 17 \t| MBD-BSSeq \t| 5127 \t| 2373 (46.3%) \t| 511 (10.0%) \t| 2243 (43.7%) \t|\n", "| 18 \t| MBD-BSSeq \t| 3278 \t| 2018 (61.6%) \t| 165 (5.0%) \t| 1095 (33.4%) \t|" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "##### Overlaps with Coding Sequences (CDS)\n", "\n", "| **Sample** \t| **Method** \t| **CpG with Data** \t| **Methylated CpG** \t| **Sparsely Methylated CpG** \t| **Unmethylated CpG** \t|\n", "|------------\t|------------\t|-------------------\t|--------------------\t|-----------------------------\t|----------------------\t|\n", "| 10 \t| WGBS \t| 63618 \t| 5918 (9.3%) \t| 7652 (12.0%) \t| 50048 (78.7%) \t|\n", "| 11 \t| WGBS \t| 67079 \t| 8085 (12.1%) \t| 7257 (10.8%) \t| 51737 (77.1%) \t|\n", "| 12 \t| WGBS \t| 209101 \t| 25530 (12.2%) \t| 16812 (8.0%) \t| 166759 (79.8%) \t|\n", "| 13 \t| RRBS \t| 190252 \t| 14708 (7.7%) \t| 10382 (5.5%) \t| 165162 (86.8%) \t|\n", "| 14 \t| RRBS \t| 151699 \t| 9279 (6.1%) \t| 8654 (5.7%) \t| 133766 (8.8%) \t|\n", "| 15 \t| RRBS \t| 186877 \t| 11132 (6.0%) \t| 12318 (6.6%) \t| 163427 (87.5%) \t|\n", "| 16 \t| MBD-BSSeq \t| 4664 \t| 2046 (43.9%) \t| 623 (13.4%) \t| 1995 (42.8%) \t|\n", "| 17 \t| MBD-BSSeq \t| 2307 \t| 758 (32.9%) \t| 220 (9.5%) \t| 1329 (57.6%) \t|\n", "| 18 \t| MBD-BSSeq \t| 1282 \t| 750 (58.5) \t| 93 (7.3%) \t| 439 (34.2%) \t|" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "##### Overalps with Introns\n", "\n", "| **Sample** \t| **Method** \t| **CpG with Data** \t| **Methylated CpG** \t| **Sparsely Methylated CpG** \t| **Unmethylated CpG** \t|\n", "|------------\t|------------\t|-------------------\t|--------------------\t|-----------------------------\t|----------------------\t|\n", "| 10 \t| WGBS \t| 96590 \t| 11106 (11.5%) \t| 8003 (8.3%) \t| 77481 (80.2%) \t|\n", "| 11 \t| WGBS \t| 99522 \t| 15088 (15.2%) \t| 7793 (7.8%) \t| 76641 (77.0%) \t|\n", "| 12 \t| WGBS \t| 425558 \t| 57278 (13.5%) \t| 27323 (6.4%) \t| 340957 (80.1%) \t|\n", "| 13 \t| RRBS \t| 798984 \t| 85069 (10.6%) \t| 35795 (4.5%) \t| 678120 (84.9%) \t|\n", "| 14 \t| RRBS \t| 629356 \t| 57748 (9.2%) \t| 30463 (4.8%) \t| 541145 (86.0%) \t|\n", "| 15 \t| RRBS \t| 778492 \t| 75177 (9.7%) \t| 41135 (5.3%) \t| 662180 (85.1%) \t|\n", "| 16 \t| MBD-BSSeq \t| 6841 \t| 4347 (63.5%) \t| 595 (8.7%) \t| 1899 (27.8%) \t|\n", "| 17 \t| MBD-BSSeq \t| 2824 \t| 1618 (57.3%) \t| 291 (10.3%) \t| 915 (32.4%) \t|\n", "| 18 \t| MBD-BSSeq \t| 2000 \t| 1270 (63.5%) \t| 73 (3.7%) \t| 657 (32.9%) \t|" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "##### Overlaps with Integenic regions\n", "\n", "| **Sample** \t| **Method** \t| **CpG with Data** \t| **Methylated CpG** \t| **Sparsely Methylated CpG** \t| **Unmethylated CpG** \t|\n", "|------------\t|------------\t|-------------------\t|--------------------\t|-----------------------------\t|----------------------\t|\n", "| 10 \t| WGBS \t| 310791 \t| 18481 (5.9%) \t| 27758 (8.9%) \t| 264552 (85.1%) \t|\n", "| 11 \t| WGBS \t| 313010 \t| 26477 (8.5%) \t| 27417 (8.8%) \t| 259116 (82.8%) \t|\n", "| 12 \t| WGBS \t| 1122745 \t| 90341 (8.0%) \t| 83053 (7.4%) \t| 949351 (84.6%) \t|\n", "| 13 \t| RRBS \t| 1957109 \t| 105044 (5.4%) \t| 83039 (4.2%) \t| 1769026 (90.4%) \t|\n", "| 14 \t| RRBS \t| 1529739 \t| 69491 (4.5%) \t| 68273 (4.5%) \t| 1391975 (91.0%) \t|\n", "| 15 \t| RRBS \t| 1909425 \t| 86666 (4.5%) \t| 92547 (4.5%) \t| 1730212 (90.6%) \t|\n", "| 16 \t| MBD-BSSeq \t| 32592 \t| 9778 (30.0%) \t| 4068 (12.5%) \t| 18746 (57.5%) \t|\n", "| 17 \t| MBD-BSSeq \t| 16670 \t| 3707 (22.2%) \t| 1771 (10.6%) \t| 11192 (67.1%) \t|\n", "| 18 \t| MBD-BSSeq \t| 11540 \t| 2819 (24.2%) \t| 1268 (11.0%) \t| 7453 (64.6%) \t|" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "## *P. acuta*" ] }, { "cell_type": "code", "execution_count": 64, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "/Users/yaaminivenkataraman/Documents/Meth_Compare/analyses/Characterizing-CpG-Methylation\n" ] } ], "source": [ "cd .." ] }, { "cell_type": "code", "execution_count": 65, "metadata": { "collapsed": true }, "outputs": [], "source": [ "#Make a directory for Pact output\n", "#!mkdir Pact" ] }, { "cell_type": "code", "execution_count": 65, "metadata": { "scrolled": true }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "/Users/yaaminivenkataraman/Documents/Meth_Compare/analyses/Characterizing-CpG-Methylation/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": 66, "metadata": { "collapsed": true }, "outputs": [], "source": [ "paGenes = \"../../../genome-feature-files/Pact.GFFannotation.Genes.gff\"" ] }, { "cell_type": "code", "execution_count": 67, "metadata": { "collapsed": true }, "outputs": [], "source": [ "paCDS = \"../../../genome-feature-files/Pact.GFFannotation.CDS.gff\"" ] }, { "cell_type": "code", "execution_count": 68, "metadata": { "collapsed": true }, "outputs": [], "source": [ "paIntron = \"../../../genome-feature-files/Pact.GFFannotation.Intron.gff\"" ] }, { "cell_type": "code", "execution_count": 69, "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": 70, "metadata": {}, "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": 71, "metadata": {}, "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": 72, "metadata": {}, "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": 73, "metadata": { "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": 74, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ " 3434720\n", "CG motif overlaps with genes\n" ] } ], "source": [ "!{bedtoolsDirectory}intersectBed \\\n", "-u \\\n", "-a {paCGMotifs} \\\n", "-b {paGenes} \\\n", "| wc -l\n", "!echo \"CG motif overlaps with genes\"" ] }, { "cell_type": "code", "execution_count": 75, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ " 1455630\n", "CG motif overlaps with CDS\n" ] } ], "source": [ "!{bedtoolsDirectory}intersectBed \\\n", "-u \\\n", "-a {paCGMotifs} \\\n", "-b {paCDS} \\\n", "| wc -l\n", "!echo \"CG motif overlaps with CDS\"" ] }, { "cell_type": "code", "execution_count": 76, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ " 1999490\n", "CG motif overlaps with introns\n" ] } ], "source": [ "!{bedtoolsDirectory}intersectBed \\\n", "-u \\\n", "-a {paCGMotifs} \\\n", "-b {paIntron} \\\n", "| wc -l\n", "!echo \"CG motif overlaps with introns\"" ] }, { "cell_type": "code", "execution_count": 77, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ " 5720900\n", "CG motif overlaps that do not overlap with genes (i.e. intergenic regions)\n" ] } ], "source": [ "!{bedtoolsDirectory}intersectBed \\\n", "-v \\\n", "-a {paCGMotifs} \\\n", "-b {paGenes} \\\n", "| wc -l\n", "!echo \"CG motif overlaps that do not overlap with genes (i.e. intergenic regions)\"" ] }, { "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", "| Intergenic Regions \t| N/A \t| 5720900 \t| 59.3 \t|" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "### 2. Download coverage files" ] }, { "cell_type": "code", "execution_count": 78, "metadata": { "scrolled": true }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "--2020-04-13 13:48:07-- https://gannet.fish.washington.edu/seashell/bu-mox/scrubbed/031520-TG-bs/Pact_tg/dedup/\n", "Resolving gannet.fish.washington.edu... 128.95.149.52\n", "Connecting to 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 0.1s \n", "\n", "2020-04-13 13:48:09 (363 KB/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", "--2020-04-13 13:48:09-- 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", "2020-04-13 13:48:09 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", "--2020-04-13 13:48:09-- 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 0.1s \n", "\n", "2020-04-13 13:48:10 (299 KB/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", "--2020-04-13 13:48:10-- 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 0.09s \n", "\n", "2020-04-13 13:48:11 (456 KB/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", "--2020-04-13 13:48:11-- 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 0.1s \n", "\n", "2020-04-13 13:48:12 (380 KB/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", "--2020-04-13 13:48:12-- 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 0.1s \n", "\n", "2020-04-13 13:48:14 (358 KB/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", "--2020-04-13 13:48:14-- https://gannet.fish.washington.edu/seashell/bu-mox/scrubbed/031520-TG-bs/Pact_tg/dedup/Meth1_R1_001_val_1_bismark_bt2_pe._10x.bedgraph\n", "Reusing existing connection to gannet.fish.washington.edu:443.\n", "HTTP request sent, awaiting response... 200 OK\n", "Length: 102637489 (98M)\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._10x.bedgraph’\n", "\n", "gannet.fish.washing 100%[===================>] 97.88M 2.34MB/s in 67s \n", "\n", "2020-04-13 13:49:20 (1.47 MB/s) - ‘gannet.fish.washington.edu/seashell/bu-mox/scrubbed/031520-TG-bs/Pact_tg/dedup/Meth1_R1_001_val_1_bismark_bt2_pe._10x.bedgraph’ saved [102637489/102637489]\n", "\n", "--2020-04-13 13:49:20-- https://gannet.fish.washington.edu/seashell/bu-mox/scrubbed/031520-TG-bs/Pact_tg/dedup/Meth2_R1_001_val_1_bismark_bt2_pe._10x.bedgraph\n", "Reusing existing connection to gannet.fish.washington.edu:443.\n", "HTTP request sent, awaiting response... 200 OK\n", "Length: 160487648 (153M)\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._10x.bedgraph’\n", "\n", "gannet.fish.washing 100%[===================>] 153.05M 1.95MB/s in 75s \n", "\n", "2020-04-13 13:50:35 (2.05 MB/s) - ‘gannet.fish.washington.edu/seashell/bu-mox/scrubbed/031520-TG-bs/Pact_tg/dedup/Meth2_R1_001_val_1_bismark_bt2_pe._10x.bedgraph’ saved [160487648/160487648]\n", "\n", "--2020-04-13 13:50:35-- https://gannet.fish.washington.edu/seashell/bu-mox/scrubbed/031520-TG-bs/Pact_tg/dedup/Meth3_R1_001_val_1_bismark_bt2_pe._10x.bedgraph\n", "Reusing existing connection to gannet.fish.washington.edu:443.\n", "HTTP request sent, awaiting response... 200 OK\n", "Length: 123612124 (118M)\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._10x.bedgraph’\n", "\n", "gannet.fish.washing 100%[===================>] 117.88M 1.61MB/s in 62s \n", "\n", "2020-04-13 13:51:37 (1.92 MB/s) - ‘gannet.fish.washington.edu/seashell/bu-mox/scrubbed/031520-TG-bs/Pact_tg/dedup/Meth3_R1_001_val_1_bismark_bt2_pe._10x.bedgraph’ saved [123612124/123612124]\n", "\n", "--2020-04-13 13:51:37-- https://gannet.fish.washington.edu/seashell/bu-mox/scrubbed/031520-TG-bs/Pact_tg/dedup/Meth7_R1_001_val_1_bismark_bt2_pe._10x.bedgraph\n", "Reusing existing connection to gannet.fish.washington.edu:443.\n", "HTTP request sent, awaiting response... 200 OK\n", "Length: 30054047 (29M)\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._10x.bedgraph’\n", "\n", "gannet.fish.washing 100%[===================>] 28.66M 2.31MB/s in 13s \n", "\n", "2020-04-13 13:51:50 (2.17 MB/s) - ‘gannet.fish.washington.edu/seashell/bu-mox/scrubbed/031520-TG-bs/Pact_tg/dedup/Meth7_R1_001_val_1_bismark_bt2_pe._10x.bedgraph’ saved [30054047/30054047]\n", "\n", "--2020-04-13 13:51:50-- https://gannet.fish.washington.edu/seashell/bu-mox/scrubbed/031520-TG-bs/Pact_tg/dedup/Meth8_R1_001_val_1_bismark_bt2_pe._10x.bedgraph\n", "Reusing existing connection to gannet.fish.washington.edu:443.\n", "HTTP request sent, awaiting response... 200 OK\n", "Length: 10067035 (9.6M)\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._10x.bedgraph’\n", "\n", "gannet.fish.washing 100%[===================>] 9.60M 1.93MB/s in 5.3s \n", "\n", "2020-04-13 13:51:56 (1.82 MB/s) - ‘gannet.fish.washington.edu/seashell/bu-mox/scrubbed/031520-TG-bs/Pact_tg/dedup/Meth8_R1_001_val_1_bismark_bt2_pe._10x.bedgraph’ saved [10067035/10067035]\n", "\n", "--2020-04-13 13:51:56-- https://gannet.fish.washington.edu/seashell/bu-mox/scrubbed/031520-TG-bs/Pact_tg/dedup/Meth9_R1_001_val_1_bismark_bt2_pe._10x.bedgraph\n", "Reusing existing connection to gannet.fish.washington.edu:443.\n", "HTTP request sent, awaiting response... 200 OK\n", "Length: 29322032 (28M)\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._10x.bedgraph’\n", "\n", "gannet.fish.washing 100%[===================>] 27.96M 2.27MB/s in 14s \n", "\n", "2020-04-13 13:52:09 (2.05 MB/s) - ‘gannet.fish.washington.edu/seashell/bu-mox/scrubbed/031520-TG-bs/Pact_tg/dedup/Meth9_R1_001_val_1_bismark_bt2_pe._10x.bedgraph’ saved [29322032/29322032]\n", "\n", "FINISHED --2020-04-13 13:52:09--\n", "Total wall clock time: 4m 2s\n", "Downloaded: 11 files, 435M in 3m 56s (1.85 MB/s)\n" ] } ], "source": [ "#Download Pact WGBS and MBD-BS 10x sample bedgraphs\n", "!wget -r -l1 --no-parent -A \"*10x.bedgraph\" https://gannet.fish.washington.edu/seashell/bu-mox/scrubbed/031520-TG-bs/Pact_tg/dedup/" ] }, { "cell_type": "code", "execution_count": 79, "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": 80, "metadata": { "collapsed": true }, "outputs": [], "source": [ "#Remove empty directory\n", "!rm -r gannet.fish.washington.edu/" ] }, { "cell_type": "code", "execution_count": 81, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "Meth1_R1_001_val_1_bismark_bt2_pe._10x.bedgraph\r\n", "Meth2_R1_001_val_1_bismark_bt2_pe._10x.bedgraph\r\n", "Meth3_R1_001_val_1_bismark_bt2_pe._10x.bedgraph\r\n", "Meth7_R1_001_val_1_bismark_bt2_pe._10x.bedgraph\r\n", "Meth8_R1_001_val_1_bismark_bt2_pe._10x.bedgraph\r\n", "Meth9_R1_001_val_1_bismark_bt2_pe._10x.bedgraph\r\n" ] } ], "source": [ "#Check files\n", "!find *bedgraph" ] }, { "cell_type": "code", "execution_count": 82, "metadata": { "scrolled": true }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "--2020-04-13 13:53:24-- https://gannet.fish.washington.edu/seashell/bu-mox/scrubbed/031520-TG-bs/Pact_tg/nodedup/\n", "Resolving gannet.fish.washington.edu... 128.95.149.52\n", "Connecting to 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 0.05s \n", "\n", "2020-04-13 13:53:24 (424 KB/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", "--2020-04-13 13:53:24-- 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", "2020-04-13 13:53:24 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", "--2020-04-13 13:53:24-- 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 0.05s \n", "\n", "2020-04-13 13:53:25 (355 KB/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", "--2020-04-13 13:53:25-- 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 0.04s \n", "\n", "2020-04-13 13:53:25 (436 KB/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", "--2020-04-13 13:53:25-- 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 0.05s \n", "\n", "2020-04-13 13:53:26 (391 KB/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", "--2020-04-13 13:53:26-- 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 0.05s \n", "\n", "2020-04-13 13:53:26 (427 KB/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", "--2020-04-13 13:53:26-- https://gannet.fish.washington.edu/seashell/bu-mox/scrubbed/031520-TG-bs/Pact_tg/nodedup/Meth4_R1_001_val_1_bismark_bt2_pe._10x.bedgraph\n", "Reusing existing connection to gannet.fish.washington.edu:443.\n", "HTTP request sent, awaiting response... 200 OK\n", "Length: 48159792 (46M)\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._10x.bedgraph’\n", "\n", "gannet.fish.washing 100%[===================>] 45.93M 1.90MB/s in 25s \n", "\n", "2020-04-13 13:53:51 (1.82 MB/s) - ‘gannet.fish.washington.edu/seashell/bu-mox/scrubbed/031520-TG-bs/Pact_tg/nodedup/Meth4_R1_001_val_1_bismark_bt2_pe._10x.bedgraph’ saved [48159792/48159792]\n", "\n", "--2020-04-13 13:53:51-- https://gannet.fish.washington.edu/seashell/bu-mox/scrubbed/031520-TG-bs/Pact_tg/nodedup/Meth5_R1_001_val_1_bismark_bt2_pe._10x.bedgraph\n", "Reusing existing connection to gannet.fish.washington.edu:443.\n", "HTTP request sent, awaiting response... 200 OK\n", "Length: 40261499 (38M)\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._10x.bedgraph’\n", "\n", "gannet.fish.washing 100%[===================>] 38.40M 1.96MB/s in 25s \n", "\n", "2020-04-13 13:54:17 (1.52 MB/s) - ‘gannet.fish.washington.edu/seashell/bu-mox/scrubbed/031520-TG-bs/Pact_tg/nodedup/Meth5_R1_001_val_1_bismark_bt2_pe._10x.bedgraph’ saved [40261499/40261499]\n", "\n", "--2020-04-13 13:54:17-- https://gannet.fish.washington.edu/seashell/bu-mox/scrubbed/031520-TG-bs/Pact_tg/nodedup/Meth6_R1_001_val_1_bismark_bt2_pe._10x.bedgraph\n", "Reusing existing connection to gannet.fish.washington.edu:443.\n", "HTTP request sent, awaiting response... 200 OK\n", "Length: 41203176 (39M)\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._10x.bedgraph’\n", "\n", "gannet.fish.washing 100%[===================>] 39.29M 1.97MB/s in 18s \n", "\n", "2020-04-13 13:54:35 (2.13 MB/s) - ‘gannet.fish.washington.edu/seashell/bu-mox/scrubbed/031520-TG-bs/Pact_tg/nodedup/Meth6_R1_001_val_1_bismark_bt2_pe._10x.bedgraph’ saved [41203176/41203176]\n", "\n", "FINISHED --2020-04-13 13:54:35--\n", "Total wall clock time: 1m 12s\n", "Downloaded: 8 files, 124M in 1m 9s (1.79 MB/s)\n" ] } ], "source": [ "#Download Pact RRBS 10x sample bedgraphs\n", "!wget -r -l1 --no-parent -A \"*10x.bedgraph\" https://gannet.fish.washington.edu/seashell/bu-mox/scrubbed/031520-TG-bs/Pact_tg/nodedup/" ] }, { "cell_type": "code", "execution_count": 83, "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": 84, "metadata": { "collapsed": true }, "outputs": [], "source": [ "#Remove empty directory\n", "!rm -r gannet.fish.washington.edu/" ] }, { "cell_type": "code", "execution_count": 85, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "Meth1_R1_001_val_1_bismark_bt2_pe._10x.bedgraph\r\n", "Meth2_R1_001_val_1_bismark_bt2_pe._10x.bedgraph\r\n", "Meth3_R1_001_val_1_bismark_bt2_pe._10x.bedgraph\r\n", "Meth4_R1_001_val_1_bismark_bt2_pe._10x.bedgraph\r\n", "Meth5_R1_001_val_1_bismark_bt2_pe._10x.bedgraph\r\n", "Meth6_R1_001_val_1_bismark_bt2_pe._10x.bedgraph\r\n", "Meth7_R1_001_val_1_bismark_bt2_pe._10x.bedgraph\r\n", "Meth8_R1_001_val_1_bismark_bt2_pe._10x.bedgraph\r\n", "Meth9_R1_001_val_1_bismark_bt2_pe._10x.bedgraph\r\n" ] } ], "source": [ "!find *bedgraph" ] }, { "cell_type": "code", "execution_count": null, "metadata": {}, "outputs": [], "source": [ "#Verify checksums from gannet\n", "!md5sum -c ../Pact-10xbedgraph-GANNET-md5sum.txt" ] }, { "cell_type": "code", "execution_count": 96, "metadata": { "scrolled": true }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ " 2518069 Meth1_R1_001_val_1_bismark_bt2_pe._10x.bedgraph\n", " 3926923 Meth2_R1_001_val_1_bismark_bt2_pe._10x.bedgraph\n", " 3028012 Meth3_R1_001_val_1_bismark_bt2_pe._10x.bedgraph\n", " 1184293 Meth4_R1_001_val_1_bismark_bt2_pe._10x.bedgraph\n", " 992337 Meth5_R1_001_val_1_bismark_bt2_pe._10x.bedgraph\n", " 1014588 Meth6_R1_001_val_1_bismark_bt2_pe._10x.bedgraph\n", " 744052 Meth7_R1_001_val_1_bismark_bt2_pe._10x.bedgraph\n", " 250032 Meth8_R1_001_val_1_bismark_bt2_pe._10x.bedgraph\n", " 725079 Meth9_R1_001_val_1_bismark_bt2_pe._10x.bedgraph\n", " 14383385 total\n" ] } ], "source": [ "!wc -l *bedgraph" ] }, { "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": 86, "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": 87, "metadata": { "scrolled": true }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "==> Meth1_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-Meth <==\r\n", "scaffold7_cov100 6144 6146 100.000000\r\n", "scaffold7_cov100 6188 6190 100.000000\r\n", "scaffold7_cov100 7438 7440 100.000000\r\n", "scaffold7_cov100 7891 7893 100.000000\r\n", "scaffold7_cov100 8323 8325 100.000000\r\n", "scaffold7_cov100 9877 9879 92.857143\r\n", "scaffold7_cov100 10216 10218 100.000000\r\n", "scaffold7_cov100 16910 16912 80.000000\r\n", "scaffold7_cov100 17090 17092 80.000000\r\n", "scaffold7_cov100 17461 17463 58.333333\r\n", "\r\n", "==> Meth2_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-Meth <==\r\n", "scaffold7_cov100 5500 5502 62.500000\r\n", "scaffold7_cov100 6144 6146 100.000000\r\n", "scaffold7_cov100 6188 6190 94.117647\r\n", "scaffold7_cov100 6198 6200 100.000000\r\n", "scaffold7_cov100 6231 6233 71.428571\r\n", "scaffold7_cov100 6233 6235 100.000000\r\n", "scaffold7_cov100 7438 7440 88.235294\r\n", "scaffold7_cov100 7696 7698 95.833333\r\n", "scaffold7_cov100 7796 7798 60.000000\r\n", "scaffold7_cov100 7891 7893 96.153846\r\n", "\r\n", "==> Meth3_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-Meth <==\r\n", "scaffold7_cov100 7438 7440 100.000000\r\n", "scaffold7_cov100 7696 7698 100.000000\r\n", "scaffold7_cov100 7796 7798 81.818182\r\n", "scaffold7_cov100 9877 9879 88.888889\r\n", "scaffold7_cov100 10273 10275 80.000000\r\n", "scaffold7_cov100 11043 11045 100.000000\r\n", "scaffold7_cov100 13385 13387 92.857143\r\n", "scaffold7_cov100 17527 17529 100.000000\r\n", "scaffold7_cov100 17552 17554 92.307692\r\n", "scaffold7_cov100 17633 17635 100.000000\r\n", "\r\n", "==> Meth4_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-Meth <==\r\n", "scaffold7_cov100 96791 96793 65.000000\r\n", "scaffold7_cov100 109716 109718 60.000000\r\n", "scaffold7_cov100 338971 338973 50.000000\r\n", "scaffold7_cov100 342219 342221 50.000000\r\n", "scaffold7_cov100 360165 360167 100.000000\r\n", "scaffold7_cov100 394699 394701 76.923077\r\n", "scaffold7_cov100 403347 403349 80.000000\r\n", "scaffold7_cov100 403727 403729 60.000000\r\n", "scaffold7_cov100 440492 440494 83.018868\r\n", "scaffold7_cov100 440575 440577 90.322581\r\n", "\r\n", "==> Meth5_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-Meth <==\r\n", "scaffold7_cov100 61080 61082 57.142857\r\n", "scaffold7_cov100 96787 96789 52.631579\r\n", "scaffold7_cov100 96791 96793 60.000000\r\n", "scaffold7_cov100 96859 96861 71.428571\r\n", "scaffold7_cov100 177834 177836 50.000000\r\n", "scaffold7_cov100 177838 177840 65.517241\r\n", "scaffold7_cov100 204124 204126 83.333333\r\n", "scaffold7_cov100 253591 253593 71.428571\r\n", "scaffold7_cov100 338971 338973 61.111111\r\n", "scaffold7_cov100 346786 346788 50.000000\r\n", "\r\n", "==> Meth6_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-Meth <==\r\n", "scaffold7_cov100 281483 281485 50.000000\r\n", "scaffold7_cov100 346786 346788 53.333333\r\n", "scaffold7_cov100 360165 360167 100.000000\r\n", "scaffold7_cov100 386815 386817 60.000000\r\n", "scaffold7_cov100 386817 386819 50.000000\r\n", "scaffold7_cov100 394699 394701 95.555556\r\n", "scaffold7_cov100 403347 403349 90.909091\r\n", "scaffold7_cov100 403727 403729 83.333333\r\n", "scaffold7_cov100 426679 426681 50.000000\r\n", "scaffold7_cov100 440492 440494 95.416667\r\n", "\r\n", "==> Meth7_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-Meth <==\r", "\r\n", "scaffold3_cov83 261 263 69.444444\r\n", "scaffold3_cov83 475 477 72.727273\r\n", "scaffold3_cov83 484 486 64.705882\r\n", "scaffold3_cov83 504 506 83.333333\r\n", "scaffold7_cov100 5500 5502 70.000000\r\n", "scaffold7_cov100 5986 5988 73.333333\r\n", "scaffold7_cov100 6144 6146 96.666667\r\n", "scaffold7_cov100 6188 6190 93.181818\r\n", "scaffold7_cov100 6198 6200 95.454545\r\n", "scaffold7_cov100 6231 6233 97.142857\r\n", "\r\n", "==> Meth8_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-Meth <==\r\n", "scaffold3_cov83 475 477 63.636364\r\n", "scaffold7_cov100 5986 5988 78.947368\r\n", "scaffold7_cov100 6144 6146 95.918367\r\n", "scaffold7_cov100 6188 6190 100.000000\r\n", "scaffold7_cov100 6198 6200 97.297297\r\n", "scaffold7_cov100 6233 6235 93.103448\r\n", "scaffold7_cov100 7796 7798 72.727273\r\n", "scaffold7_cov100 7891 7893 90.000000\r\n", "scaffold7_cov100 12652 12654 96.226415\r\n", "scaffold7_cov100 12662 12664 92.079208\r\n", "\r\n", "==> Meth9_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-Meth <==\r\n", "scaffold7_cov100 5986 5988 79.166667\r\n", "scaffold7_cov100 6144 6146 96.296296\r\n", "scaffold7_cov100 6188 6190 92.592593\r\n", "scaffold7_cov100 6198 6200 94.339623\r\n", "scaffold7_cov100 6231 6233 95.555556\r\n", "scaffold7_cov100 6233 6235 97.619048\r\n", "scaffold7_cov100 7438 7440 100.000000\r\n", "scaffold7_cov100 7696 7698 91.304348\r\n", "scaffold7_cov100 7796 7798 100.000000\r\n", "scaffold7_cov100 7891 7893 92.857143\r\n" ] } ], "source": [ "!head *Meth" ] }, { "cell_type": "code", "execution_count": 88, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ " 37201 Meth1_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-Meth\n", " 66524 Meth2_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-Meth\n", " 51081 Meth3_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-Meth\n", " 12021 Meth4_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-Meth\n", " 14557 Meth5_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-Meth\n", " 10621 Meth6_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-Meth\n", " 195284 Meth7_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-Meth\n", " 156098 Meth8_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-Meth\n", " 187956 Meth9_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-Meth\n", " 731343 total\n" ] } ], "source": [ "!wc -l *Meth" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "##### Sparsely methylated loci" ] }, { "cell_type": "code", "execution_count": 89, "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": 90, "metadata": { "scrolled": true }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "==> Meth1_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-sparseMeth <==\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", "scaffold7_cov100 1293 1295 11.111111\r\n", "scaffold7_cov100 2289 2291 13.333333\r\n", "scaffold7_cov100 4481 4483 20.000000\r\n", "scaffold7_cov100 4596 4598 12.500000\r\n", "scaffold7_cov100 9715 9717 18.181818\r\n", "scaffold7_cov100 17098 17100 36.363636\r\n", "scaffold7_cov100 17952 17954 44.000000\r\n", "\r\n", "==> Meth2_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-sparseMeth <==\r\n", "scaffold6_cov64 3978 3980 11.111111\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", "scaffold7_cov100 11439 11441 40.000000\r\n", "scaffold7_cov100 13385 13387 18.750000\r\n", "scaffold7_cov100 16874 16876 18.181818\r\n", "scaffold7_cov100 17074 17076 36.363636\r\n", "scaffold7_cov100 17098 17100 35.714286\r\n", "\r\n", "==> Meth3_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-sparseMeth <==\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", "scaffold7_cov100 4630 4632 28.000000\r\n", "scaffold7_cov100 4678 4680 13.333333\r\n", "scaffold7_cov100 9715 9717 30.000000\r\n", "scaffold7_cov100 11439 11441 41.666667\r\n", "scaffold7_cov100 13450 13452 27.272727\r\n", "scaffold7_cov100 17212 17214 30.769231\r\n", "scaffold7_cov100 17952 17954 31.250000\r\n", "\r\n", "==> Meth4_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-sparseMeth <==\r\n", "scaffold6_cov64 5904 5906 15.485564\r\n", "scaffold6_cov64 6732 6734 16.666667\r\n", "scaffold7_cov100 4351 4353 46.428571\r\n", "scaffold7_cov100 39365 39367 25.000000\r\n", "scaffold7_cov100 39367 39369 25.000000\r\n", "scaffold7_cov100 40132 40134 26.666667\r\n", "scaffold7_cov100 40148 40150 21.052632\r\n", "scaffold7_cov100 40816 40818 40.000000\r\n", "scaffold7_cov100 46343 46345 21.739130\r\n", "scaffold7_cov100 46397 46399 12.500000\r\n", "\r\n", "==> Meth5_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-sparseMeth <==\r\n", "scaffold6_cov64 6374 6376 45.454545\r\n", "scaffold7_cov100 46343 46345 46.153846\r\n", "scaffold7_cov100 94139 94141 27.272727\r\n", "scaffold7_cov100 94142 94144 16.666667\r\n", "scaffold7_cov100 94939 94941 36.363636\r\n", "scaffold7_cov100 131174 131176 11.111111\r\n", "scaffold7_cov100 131309 131311 11.764706\r\n", "scaffold7_cov100 162610 162612 20.000000\r\n", "scaffold7_cov100 177836 177838 22.222222\r\n", "scaffold7_cov100 191986 191988 18.181818\r\n", "\r\n", "==> Meth6_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-sparseMeth <==\r\n", "scaffold6_cov64 5604 5606 11.538462\r\n", "scaffold6_cov64 6266 6268 14.285714\r\n", "scaffold6_cov64 6704 6706 14.285714\r\n", "scaffold7_cov100 4351 4353 10.256410\r\n", "scaffold7_cov100 32521 32523 18.750000\r\n", "scaffold7_cov100 32984 32986 13.333333\r\n", "scaffold7_cov100 37936 37938 21.428571\r\n", "scaffold7_cov100 46343 46345 47.619048\r\n", "scaffold7_cov100 61080 61082 14.285714\r\n", "scaffold7_cov100 82753 82755 12.500000\r\n", "\r\n", "==> Meth7_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-sparseMeth <==\r\n", "scaffold3_cov83 189 191 44.444444\r\n", "scaffold3_cov83 208 210 42.857143\r\n", "scaffold7_cov100 2080 2082 11.111111\r\n", "scaffold7_cov100 11439 11441 25.000000\r\n", "scaffold7_cov100 12821 12823 36.363636\r\n", "scaffold7_cov100 14042 14044 18.518519\r\n", "scaffold7_cov100 17952 17954 38.297872\r\n", "scaffold7_cov100 19493 19495 47.826087\r\n", "scaffold7_cov100 24614 24616 42.857143\r\n", "scaffold7_cov100 24617 24619 14.285714\r\n", "\r\n", "==> Meth8_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-sparseMeth <==\r\n", "scaffold3_cov83 484 486 45.454545\r\n", "scaffold7_cov100 5500 5502 11.764706\r\n", "scaffold7_cov100 6231 6233 42.857143\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", "scaffold7_cov100 24494 24496 17.647059\r\n", "scaffold7_cov100 92055 92057 26.666667\r\n", "scaffold7_cov100 92105 92107 41.666667\r\n", "\r\n", "==> Meth9_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-sparseMeth <==\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", "scaffold7_cov100 10755 10757 15.000000\r\n", "scaffold7_cov100 12683 12685 40.000000\r\n", "scaffold7_cov100 13275 13277 47.619048\r\n", "scaffold7_cov100 14042 14044 34.615385\r\n" ] } ], "source": [ "!head *sparseMeth" ] }, { "cell_type": "code", "execution_count": 91, "metadata": { "scrolled": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ " 83999 Meth1_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-sparseMeth\n", " 109999 Meth2_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-sparseMeth\n", " 104860 Meth3_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-sparseMeth\n", " 65647 Meth4_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-sparseMeth\n", " 27831 Meth5_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-sparseMeth\n", " 38383 Meth6_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-sparseMeth\n", " 106836 Meth7_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-sparseMeth\n", " 39889 Meth8_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-sparseMeth\n", " 112592 Meth9_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-sparseMeth\n", " 690036 total\n" ] } ], "source": [ "!wc -l *sparseMeth" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "##### Unmethylated loci" ] }, { "cell_type": "code", "execution_count": 92, "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": 93, "metadata": { "scrolled": true }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "==> Meth1_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-unMeth <==\r\n", "scaffold2_cov51 649 651 0.000000\r\n", "scaffold2_cov51 686 688 8.333333\r\n", "scaffold3_cov83 189 191 6.250000\r\n", "scaffold3_cov83 208 210 0.000000\r\n", "scaffold3_cov83 243 245 0.000000\r\n", "scaffold3_cov83 261 263 8.108108\r\n", "scaffold6_cov64 290 292 0.000000\r\n", "scaffold6_cov64 298 300 0.000000\r\n", "scaffold6_cov64 489 491 0.000000\r\n", "scaffold6_cov64 826 828 0.000000\r\n", "\r\n", "==> Meth2_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-unMeth <==\r\n", "scaffold1_cov55 169 171 0.000000\r\n", "scaffold1_cov55 194 196 0.000000\r\n", "scaffold1_cov55 250 252 0.000000\r\n", "scaffold1_cov55 291 293 0.000000\r\n", "scaffold3_cov83 189 191 8.695652\r\n", "scaffold3_cov83 208 210 6.896552\r\n", "scaffold3_cov83 243 245 0.000000\r\n", "scaffold3_cov83 261 263 7.692308\r\n", "scaffold3_cov83 475 477 4.761905\r\n", "scaffold3_cov83 484 486 7.317073\r\n", "\r\n", "==> Meth3_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-unMeth <==\r\n", "scaffold2_cov51 649 651 0.000000\r\n", "scaffold2_cov51 778 780 0.000000\r\n", "scaffold3_cov83 208 210 5.128205\r\n", "scaffold3_cov83 243 245 2.272727\r\n", "scaffold3_cov83 261 263 6.666667\r\n", "scaffold3_cov83 484 486 4.444444\r\n", "scaffold3_cov83 504 506 9.090909\r\n", "scaffold6_cov64 290 292 0.000000\r\n", "scaffold6_cov64 298 300 0.000000\r\n", "scaffold6_cov64 489 491 0.000000\r\n", "\r\n", "==> Meth4_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-unMeth <==\r\n", "scaffold6_cov64 5456 5458 0.000000\r\n", "scaffold6_cov64 5486 5488 0.000000\r\n", "scaffold6_cov64 5545 5547 0.000000\r\n", "scaffold6_cov64 5559 5561 0.000000\r\n", "scaffold6_cov64 5561 5563 2.941176\r\n", "scaffold6_cov64 5567 5569 0.000000\r\n", "scaffold6_cov64 5574 5576 0.000000\r\n", "scaffold6_cov64 5581 5583 0.000000\r\n", "scaffold6_cov64 5583 5585 0.000000\r\n", "scaffold6_cov64 5592 5594 0.000000\r\n", "\r\n", "==> Meth5_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-unMeth <==\r\n", "scaffold6_cov64 4588 4590 0.000000\r\n", "scaffold6_cov64 5559 5561 7.692308\r\n", "scaffold6_cov64 5561 5563 7.142857\r\n", "scaffold6_cov64 5567 5569 0.000000\r\n", "scaffold6_cov64 5574 5576 5.263158\r\n", "scaffold6_cov64 5581 5583 0.000000\r\n", "scaffold6_cov64 5583 5585 0.000000\r\n", "scaffold6_cov64 5592 5594 0.000000\r\n", "scaffold6_cov64 5594 5596 0.000000\r\n", "scaffold6_cov64 5604 5606 0.000000\r\n", "\r\n", "==> Meth6_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-unMeth <==\r\n", "scaffold6_cov64 5545 5547 0.000000\r\n", "scaffold6_cov64 5559 5561 4.166667\r\n", "scaffold6_cov64 5561 5563 0.000000\r\n", "scaffold6_cov64 5567 5569 0.000000\r\n", "scaffold6_cov64 5574 5576 0.000000\r\n", "scaffold6_cov64 5581 5583 8.333333\r\n", "scaffold6_cov64 5583 5585 0.000000\r\n", "scaffold6_cov64 5592 5594 0.000000\r\n", "scaffold6_cov64 5594 5596 0.000000\r\n", "scaffold6_cov64 5644 5646 2.728873\r\n", "\r\n", "==> Meth7_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-unMeth <==\r\n", "scaffold3_cov83 243 245 0.000000\r\n", "scaffold6_cov64 489 491 0.000000\r\n", "scaffold6_cov64 3343 3345 0.000000\r\n", "scaffold6_cov64 3420 3422 10.000000\r\n", "scaffold6_cov64 3435 3437 0.000000\r\n", "scaffold6_cov64 3439 3441 0.000000\r\n", "scaffold6_cov64 3444 3446 0.000000\r\n", "scaffold6_cov64 3507 3509 0.000000\r\n", "scaffold6_cov64 3569 3571 0.000000\r\n", "scaffold6_cov64 3596 3598 0.000000\r\n", "\r\n", "==> Meth8_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-unMeth <==\r\n", "scaffold6_cov64 6338 6340 0.000000\r\n", "scaffold6_cov64 6344 6346 0.000000\r\n", "scaffold6_cov64 6361 6363 0.000000\r\n", "scaffold6_cov64 6374 6376 0.000000\r\n", "scaffold6_cov64 6380 6382 0.000000\r\n", "scaffold6_cov64 6387 6389 0.000000\r\n", "scaffold7_cov100 5578 5580 0.000000\r\n", "scaffold7_cov100 12587 12589 0.840336\r\n", "scaffold7_cov100 13038 13040 3.448276\r\n", "scaffold7_cov100 17164 17166 0.000000\r\n", "\r\n", "==> Meth9_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-unMeth <==\r\n", "scaffold3_cov83 243 245 0.000000\r\n", "scaffold6_cov64 298 300 0.000000\r\n", "scaffold6_cov64 489 491 0.000000\r\n", "scaffold6_cov64 2179 2181 0.000000\r\n", "scaffold6_cov64 3412 3414 0.000000\r\n", "scaffold6_cov64 3420 3422 0.000000\r\n", "scaffold6_cov64 3439 3441 7.692308\r\n", "scaffold6_cov64 3444 3446 0.000000\r\n", "scaffold6_cov64 3507 3509 0.000000\r\n", "scaffold6_cov64 3569 3571 0.000000\r\n" ] } ], "source": [ "!head *unMeth" ] }, { "cell_type": "code", "execution_count": 94, "metadata": { "scrolled": true }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ " 2396869 Meth1_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-unMeth\n", " 3750400 Meth2_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-unMeth\n", " 2872071 Meth3_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-unMeth\n", " 1106625 Meth4_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-unMeth\n", " 949949 Meth5_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-unMeth\n", " 965584 Meth6_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-unMeth\n", " 441932 Meth7_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-unMeth\n", " 54045 Meth8_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-unMeth\n", " 424531 Meth9_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-unMeth\n", " 12962006 total\n" ] } ], "source": [ "!wc -l *unMeth" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "##### Summary" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "| **Sample** \t| **Method** \t| **CpG with Data** \t| **Methylated CpG** \t| **Sparsely Methylated CpG** \t| **Unmethylated CpG** \t|\n", "|:----------:\t|:----------:\t|:-----------------:\t|:------------------:\t|:---------------------------:\t|:--------------------:\t|\n", "| 1 \t| WGBS \t| 2518069 \t| 37201 (1.5%) \t| 83999 (3.3%) \t| 2396869 (95.2%) \t|\n", "| 2 \t| WGBS \t| 3926923 \t| 66524 (1.7%) \t| 109999 (2.8%) \t| 3750400 (95.5%) \t|\n", "| 3 \t| WGBS \t| 3028012 \t| 51081 (1.7%) \t| 104860 (3.5%) \t| 2872071 (94.9%) \t|\n", "| 4 \t| RRBS \t| 1184293 \t| 12021 (1.0%) \t| 65647 (5.5%) \t| 1106625 (93.4%) \t|\n", "| 5 \t| RRBS \t| 992337 \t| 14557 (1.5%) \t| 27831 (2.8%) \t| 949949 (95.7%) \t|\n", "| 6 \t| RRBS \t| 1014588 \t| 10621 (1.0%) \t| 38383 (3.8%) \t| 965584 (95.2%) \t|\n", "| 7 \t| MBD-BSSeq \t| 744052 \t| 195284 (26.2%) \t| 106836 (14.3%) \t| 441932 (59.4%) \t|\n", "| 8 \t| MBD-BSSeq \t| 250032 \t| 156098 (62.4%) \t| 39889 (16.0%) \t| 54045 (21.6%) \t|\n", "| 9 \t| MBD-BSSeq \t| 725079 \t| 187956 (25.9%) \t| 112592 (15.5%) \t| 424531 (58.5%) \t|" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "### 4. Characterize genomic locations of CpGs" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "#### 4a. Create BEDfiles" ] }, { "cell_type": "code", "execution_count": 97, "metadata": { "scrolled": true }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ " 2518069 Meth1_R1_001_val_1_bismark_bt2_pe._10x.bedgraph.bed\n", " 37201 Meth1_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-Meth.bed\n", " 83999 Meth1_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-sparseMeth.bed\n", " 2396869 Meth1_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-unMeth.bed\n", " 3926923 Meth2_R1_001_val_1_bismark_bt2_pe._10x.bedgraph.bed\n", " 66524 Meth2_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-Meth.bed\n", " 109999 Meth2_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-sparseMeth.bed\n", " 3750400 Meth2_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-unMeth.bed\n", " 3028012 Meth3_R1_001_val_1_bismark_bt2_pe._10x.bedgraph.bed\n", " 51081 Meth3_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-Meth.bed\n", " 104860 Meth3_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-sparseMeth.bed\n", " 2872071 Meth3_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-unMeth.bed\n", " 1184293 Meth4_R1_001_val_1_bismark_bt2_pe._10x.bedgraph.bed\n", " 12021 Meth4_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-Meth.bed\n", " 65647 Meth4_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-sparseMeth.bed\n", " 1106625 Meth4_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-unMeth.bed\n", " 992337 Meth5_R1_001_val_1_bismark_bt2_pe._10x.bedgraph.bed\n", " 14557 Meth5_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-Meth.bed\n", " 27831 Meth5_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-sparseMeth.bed\n", " 949949 Meth5_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-unMeth.bed\n", " 1014588 Meth6_R1_001_val_1_bismark_bt2_pe._10x.bedgraph.bed\n", " 10621 Meth6_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-Meth.bed\n", " 38383 Meth6_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-sparseMeth.bed\n", " 965584 Meth6_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-unMeth.bed\n", " 744052 Meth7_R1_001_val_1_bismark_bt2_pe._10x.bedgraph.bed\n", " 195284 Meth7_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-Meth.bed\n", " 106836 Meth7_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-sparseMeth.bed\n", " 441932 Meth7_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-unMeth.bed\n", " 250032 Meth8_R1_001_val_1_bismark_bt2_pe._10x.bedgraph.bed\n", " 156098 Meth8_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-Meth.bed\n", " 39889 Meth8_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-sparseMeth.bed\n", " 54045 Meth8_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-unMeth.bed\n", " 725079 Meth9_R1_001_val_1_bismark_bt2_pe._10x.bedgraph.bed\n", " 187956 Meth9_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-Meth.bed\n", " 112592 Meth9_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-sparseMeth.bed\n", " 424531 Meth9_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-unMeth.bed\n" ] } ], "source": [ "%%bash\n", "\n", "for f in *bedgraph*\n", "do\n", " awk '{print $1\"\\t\"$2\"\\t\"$3}' ${f} > ${f}.bed\n", " wc -l ${f}.bed\n", "done" ] }, { "cell_type": "code", "execution_count": 98, "metadata": { "scrolled": true }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "Meth1_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-Meth.bed\r\n", "Meth1_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-sparseMeth.bed\r\n", "Meth1_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-unMeth.bed\r\n", "Meth1_R1_001_val_1_bismark_bt2_pe._10x.bedgraph.bed\r\n", "Meth2_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-Meth.bed\r\n", "Meth2_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-sparseMeth.bed\r\n", "Meth2_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-unMeth.bed\r\n", "Meth2_R1_001_val_1_bismark_bt2_pe._10x.bedgraph.bed\r\n", "Meth3_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-Meth.bed\r\n", "Meth3_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-sparseMeth.bed\r\n", "Meth3_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-unMeth.bed\r\n", "Meth3_R1_001_val_1_bismark_bt2_pe._10x.bedgraph.bed\r\n", "Meth4_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-Meth.bed\r\n", "Meth4_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-sparseMeth.bed\r\n", "Meth4_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-unMeth.bed\r\n", "Meth4_R1_001_val_1_bismark_bt2_pe._10x.bedgraph.bed\r\n", "Meth5_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-Meth.bed\r\n", "Meth5_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-sparseMeth.bed\r\n", "Meth5_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-unMeth.bed\r\n", "Meth5_R1_001_val_1_bismark_bt2_pe._10x.bedgraph.bed\r\n", "Meth6_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-Meth.bed\r\n", "Meth6_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-sparseMeth.bed\r\n", "Meth6_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-unMeth.bed\r\n", "Meth6_R1_001_val_1_bismark_bt2_pe._10x.bedgraph.bed\r\n", "Meth7_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-Meth.bed\r\n", "Meth7_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-sparseMeth.bed\r\n", "Meth7_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-unMeth.bed\r\n", "Meth7_R1_001_val_1_bismark_bt2_pe._10x.bedgraph.bed\r\n", "Meth8_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-Meth.bed\r\n", "Meth8_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-sparseMeth.bed\r\n", "Meth8_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-unMeth.bed\r\n", "Meth8_R1_001_val_1_bismark_bt2_pe._10x.bedgraph.bed\r\n", "Meth9_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-Meth.bed\r\n", "Meth9_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-sparseMeth.bed\r\n", "Meth9_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-unMeth.bed\r\n", "Meth9_R1_001_val_1_bismark_bt2_pe._10x.bedgraph.bed\r\n" ] } ], "source": [ "#Confirm BEDfile creation\n", "!find *.bed" ] }, { "cell_type": "code", "execution_count": 99, "metadata": { "scrolled": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "scaffold2_cov51\t649\t651\r\n", "scaffold2_cov51\t686\t688\r\n", "scaffold3_cov83\t189\t191\r\n", "scaffold3_cov83\t208\t210\r\n", "scaffold3_cov83\t243\t245\r\n", "scaffold3_cov83\t261\t263\r\n", "scaffold3_cov83\t475\t477\r\n", "scaffold3_cov83\t484\t486\r\n", "scaffold3_cov83\t504\t506\r\n", "scaffold6_cov64\t290\t292\r\n" ] } ], "source": [ "#Confirm file creation\n", "!head Meth1_R1_001_val_1_bismark_bt2_pe._10x.bedgraph.bed" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "#### 4b. Genes" ] }, { "cell_type": "code", "execution_count": 102, "metadata": { "collapsed": true, "scrolled": true }, "outputs": [], "source": [ "%%bash\n", "\n", "for f in *bed\n", "do\n", " /usr/local/bin/intersectBed \\\n", " -wb \\\n", " -a ${f} \\\n", " -b ../../../genome-feature-files/Pact.GFFannotation.Genes.gff \\\n", " > ${f}-paGenes\n", "done" ] }, { "cell_type": "code", "execution_count": 103, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "==> Meth1_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-Meth.bed-paGenes <==\r\n", "scaffold7_cov100\t6144\t6146\tscaffold7_cov100\tAUGUSTUS\tgene\t3467\t6217\t0.78\t-\t.\tg4\r\n", "scaffold7_cov100\t6188\t6190\tscaffold7_cov100\tAUGUSTUS\tgene\t3467\t6217\t0.78\t-\t.\tg4\r\n", "scaffold7_cov100\t7438\t7440\tscaffold7_cov100\tAUGUSTUS\tgene\t7069\t9073\t1\t-\t.\tg5\r\n", "scaffold7_cov100\t7891\t7893\tscaffold7_cov100\tAUGUSTUS\tgene\t7069\t9073\t1\t-\t.\tg5\r\n", "scaffold7_cov100\t8323\t8325\tscaffold7_cov100\tAUGUSTUS\tgene\t7069\t9073\t1\t-\t.\tg5\r\n", "scaffold7_cov100\t9877\t9879\tscaffold7_cov100\tAUGUSTUS\tgene\t9590\t11670\t0.8\t-\t.\tg6\r\n", "scaffold7_cov100\t10216\t10218\tscaffold7_cov100\tAUGUSTUS\tgene\t9590\t11670\t0.8\t-\t.\tg6\r\n", "scaffold7_cov100\t16910\t16912\tscaffold7_cov100\tAUGUSTUS\tgene\t15738\t18320\t0.96\t+\t.\tg8\r\n", "scaffold7_cov100\t17090\t17092\tscaffold7_cov100\tAUGUSTUS\tgene\t15738\t18320\t0.96\t+\t.\tg8\r\n", "scaffold7_cov100\t17461\t17463\tscaffold7_cov100\tAUGUSTUS\tgene\t15738\t18320\t0.96\t+\t.\tg8\r\n", "\r\n", "==> Meth1_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-sparseMeth.bed-paGenes <==\r\n", "scaffold7_cov100\t1293\t1295\tscaffold7_cov100\tAUGUSTUS\tgene\t1\t2566\t0.96\t+\t.\tg3\r\n", "scaffold7_cov100\t2289\t2291\tscaffold7_cov100\tAUGUSTUS\tgene\t1\t2566\t0.96\t+\t.\tg3\r\n", "scaffold7_cov100\t4481\t4483\tscaffold7_cov100\tAUGUSTUS\tgene\t3467\t6217\t0.78\t-\t.\tg4\r\n", "scaffold7_cov100\t4596\t4598\tscaffold7_cov100\tAUGUSTUS\tgene\t3467\t6217\t0.78\t-\t.\tg4\r\n", "scaffold7_cov100\t9715\t9717\tscaffold7_cov100\tAUGUSTUS\tgene\t9590\t11670\t0.8\t-\t.\tg6\r\n", "scaffold7_cov100\t17098\t17100\tscaffold7_cov100\tAUGUSTUS\tgene\t15738\t18320\t0.96\t+\t.\tg8\r\n", "scaffold7_cov100\t17952\t17954\tscaffold7_cov100\tAUGUSTUS\tgene\t15738\t18320\t0.96\t+\t.\tg8\r\n", "scaffold7_cov100\t20473\t20475\tscaffold7_cov100\tAUGUSTUS\tgene\t20078\t24295\t0.39\t+\t.\tg11\r\n", "scaffold7_cov100\t29019\t29021\tscaffold7_cov100\tAUGUSTUS\tgene\t28517\t29779\t0.69\t-\t.\tg12\r\n", "scaffold7_cov100\t45742\t45744\tscaffold7_cov100\tAUGUSTUS\tgene\t41188\t47537\t0.97\t+\t.\tg14\r\n", "\r\n", "==> Meth1_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-unMeth.bed-paGenes <==\r\n", "scaffold6_cov64\t290\t292\tscaffold6_cov64\tAUGUSTUS\tgene\t1\t5652\t0.46\t-\t.\tg1\r\n", "scaffold6_cov64\t298\t300\tscaffold6_cov64\tAUGUSTUS\tgene\t1\t5652\t0.46\t-\t.\tg1\r\n", "scaffold6_cov64\t489\t491\tscaffold6_cov64\tAUGUSTUS\tgene\t1\t5652\t0.46\t-\t.\tg1\r\n", "scaffold6_cov64\t826\t828\tscaffold6_cov64\tAUGUSTUS\tgene\t1\t5652\t0.46\t-\t.\tg1\r\n", "scaffold6_cov64\t2179\t2181\tscaffold6_cov64\tAUGUSTUS\tgene\t1\t5652\t0.46\t-\t.\tg1\r\n", "scaffold6_cov64\t2805\t2807\tscaffold6_cov64\tAUGUSTUS\tgene\t1\t5652\t0.46\t-\t.\tg1\r\n", "scaffold6_cov64\t2876\t2878\tscaffold6_cov64\tAUGUSTUS\tgene\t1\t5652\t0.46\t-\t.\tg1\r\n", "scaffold6_cov64\t3006\t3008\tscaffold6_cov64\tAUGUSTUS\tgene\t1\t5652\t0.46\t-\t.\tg1\r\n", "scaffold6_cov64\t3054\t3056\tscaffold6_cov64\tAUGUSTUS\tgene\t1\t5652\t0.46\t-\t.\tg1\r\n", "scaffold6_cov64\t3058\t3060\tscaffold6_cov64\tAUGUSTUS\tgene\t1\t5652\t0.46\t-\t.\tg1\r\n", "\r\n", "==> Meth1_R1_001_val_1_bismark_bt2_pe._10x.bedgraph.bed-paGenes <==\r\n", "scaffold6_cov64\t290\t292\tscaffold6_cov64\tAUGUSTUS\tgene\t1\t5652\t0.46\t-\t.\tg1\r\n", "scaffold6_cov64\t298\t300\tscaffold6_cov64\tAUGUSTUS\tgene\t1\t5652\t0.46\t-\t.\tg1\r\n", "scaffold6_cov64\t489\t491\tscaffold6_cov64\tAUGUSTUS\tgene\t1\t5652\t0.46\t-\t.\tg1\r\n", "scaffold6_cov64\t826\t828\tscaffold6_cov64\tAUGUSTUS\tgene\t1\t5652\t0.46\t-\t.\tg1\r\n", "scaffold6_cov64\t2179\t2181\tscaffold6_cov64\tAUGUSTUS\tgene\t1\t5652\t0.46\t-\t.\tg1\r\n", "scaffold6_cov64\t2805\t2807\tscaffold6_cov64\tAUGUSTUS\tgene\t1\t5652\t0.46\t-\t.\tg1\r\n", "scaffold6_cov64\t2876\t2878\tscaffold6_cov64\tAUGUSTUS\tgene\t1\t5652\t0.46\t-\t.\tg1\r\n", "scaffold6_cov64\t3006\t3008\tscaffold6_cov64\tAUGUSTUS\tgene\t1\t5652\t0.46\t-\t.\tg1\r\n", "scaffold6_cov64\t3054\t3056\tscaffold6_cov64\tAUGUSTUS\tgene\t1\t5652\t0.46\t-\t.\tg1\r\n", "scaffold6_cov64\t3058\t3060\tscaffold6_cov64\tAUGUSTUS\tgene\t1\t5652\t0.46\t-\t.\tg1\r\n", "\r\n", "==> Meth2_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-Meth.bed-paGenes <==\r\n", "scaffold7_cov100\t5500\t5502\tscaffold7_cov100\tAUGUSTUS\tgene\t3467\t6217\t0.78\t-\t.\tg4\r\n", "scaffold7_cov100\t6144\t6146\tscaffold7_cov100\tAUGUSTUS\tgene\t3467\t6217\t0.78\t-\t.\tg4\r\n", "scaffold7_cov100\t6188\t6190\tscaffold7_cov100\tAUGUSTUS\tgene\t3467\t6217\t0.78\t-\t.\tg4\r\n", "scaffold7_cov100\t6198\t6200\tscaffold7_cov100\tAUGUSTUS\tgene\t3467\t6217\t0.78\t-\t.\tg4\r\n", "scaffold7_cov100\t7438\t7440\tscaffold7_cov100\tAUGUSTUS\tgene\t7069\t9073\t1\t-\t.\tg5\r\n", "scaffold7_cov100\t7696\t7698\tscaffold7_cov100\tAUGUSTUS\tgene\t7069\t9073\t1\t-\t.\tg5\r\n", "scaffold7_cov100\t7796\t7798\tscaffold7_cov100\tAUGUSTUS\tgene\t7069\t9073\t1\t-\t.\tg5\r\n", "scaffold7_cov100\t7891\t7893\tscaffold7_cov100\tAUGUSTUS\tgene\t7069\t9073\t1\t-\t.\tg5\r\n", "scaffold7_cov100\t9877\t9879\tscaffold7_cov100\tAUGUSTUS\tgene\t9590\t11670\t0.8\t-\t.\tg6\r\n", "scaffold7_cov100\t10216\t10218\tscaffold7_cov100\tAUGUSTUS\tgene\t9590\t11670\t0.8\t-\t.\tg6\r\n", "\r\n", "==> Meth2_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-sparseMeth.bed-paGenes <==\r\n", "scaffold6_cov64\t3978\t3980\tscaffold6_cov64\tAUGUSTUS\tgene\t1\t5652\t0.46\t-\t.\tg1\r\n", "scaffold7_cov100\t3994\t3996\tscaffold7_cov100\tAUGUSTUS\tgene\t3467\t6217\t0.78\t-\t.\tg4\r\n", "scaffold7_cov100\t7121\t7123\tscaffold7_cov100\tAUGUSTUS\tgene\t7069\t9073\t1\t-\t.\tg5\r\n", "scaffold7_cov100\t7201\t7203\tscaffold7_cov100\tAUGUSTUS\tgene\t7069\t9073\t1\t-\t.\tg5\r\n", "scaffold7_cov100\t10755\t10757\tscaffold7_cov100\tAUGUSTUS\tgene\t9590\t11670\t0.8\t-\t.\tg6\r\n", "scaffold7_cov100\t11439\t11441\tscaffold7_cov100\tAUGUSTUS\tgene\t9590\t11670\t0.8\t-\t.\tg6\r\n", "scaffold7_cov100\t13385\t13387\tscaffold7_cov100\tAUGUSTUS\tgene\t13339\t15463\t0.92\t-\t.\tg7\r\n", "scaffold7_cov100\t16874\t16876\tscaffold7_cov100\tAUGUSTUS\tgene\t15738\t18320\t0.96\t+\t.\tg8\r\n", "scaffold7_cov100\t17074\t17076\tscaffold7_cov100\tAUGUSTUS\tgene\t15738\t18320\t0.96\t+\t.\tg8\r\n", "scaffold7_cov100\t17098\t17100\tscaffold7_cov100\tAUGUSTUS\tgene\t15738\t18320\t0.96\t+\t.\tg8\r\n", "\r\n", "==> Meth2_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-unMeth.bed-paGenes <==\r\n", "scaffold6_cov64\t290\t292\tscaffold6_cov64\tAUGUSTUS\tgene\t1\t5652\t0.46\t-\t.\tg1\r\n", "scaffold6_cov64\t298\t300\tscaffold6_cov64\tAUGUSTUS\tgene\t1\t5652\t0.46\t-\t.\tg1\r\n", "scaffold6_cov64\t489\t491\tscaffold6_cov64\tAUGUSTUS\tgene\t1\t5652\t0.46\t-\t.\tg1\r\n", "scaffold6_cov64\t826\t828\tscaffold6_cov64\tAUGUSTUS\tgene\t1\t5652\t0.46\t-\t.\tg1\r\n", "scaffold6_cov64\t1725\t1727\tscaffold6_cov64\tAUGUSTUS\tgene\t1\t5652\t0.46\t-\t.\tg1\r\n", "scaffold6_cov64\t2097\t2099\tscaffold6_cov64\tAUGUSTUS\tgene\t1\t5652\t0.46\t-\t.\tg1\r\n", "scaffold6_cov64\t2179\t2181\tscaffold6_cov64\tAUGUSTUS\tgene\t1\t5652\t0.46\t-\t.\tg1\r\n", "scaffold6_cov64\t2253\t2255\tscaffold6_cov64\tAUGUSTUS\tgene\t1\t5652\t0.46\t-\t.\tg1\r\n", "scaffold6_cov64\t2676\t2678\tscaffold6_cov64\tAUGUSTUS\tgene\t1\t5652\t0.46\t-\t.\tg1\r\n", "scaffold6_cov64\t2682\t2684\tscaffold6_cov64\tAUGUSTUS\tgene\t1\t5652\t0.46\t-\t.\tg1\r\n", "\r\n", "==> Meth2_R1_001_val_1_bismark_bt2_pe._10x.bedgraph.bed-paGenes <==\r\n", "scaffold6_cov64\t290\t292\tscaffold6_cov64\tAUGUSTUS\tgene\t1\t5652\t0.46\t-\t.\tg1\r\n", "scaffold6_cov64\t298\t300\tscaffold6_cov64\tAUGUSTUS\tgene\t1\t5652\t0.46\t-\t.\tg1\r\n", "scaffold6_cov64\t489\t491\tscaffold6_cov64\tAUGUSTUS\tgene\t1\t5652\t0.46\t-\t.\tg1\r\n", "scaffold6_cov64\t826\t828\tscaffold6_cov64\tAUGUSTUS\tgene\t1\t5652\t0.46\t-\t.\tg1\r\n", "scaffold6_cov64\t1725\t1727\tscaffold6_cov64\tAUGUSTUS\tgene\t1\t5652\t0.46\t-\t.\tg1\r\n", "scaffold6_cov64\t2097\t2099\tscaffold6_cov64\tAUGUSTUS\tgene\t1\t5652\t0.46\t-\t.\tg1\r\n", "scaffold6_cov64\t2179\t2181\tscaffold6_cov64\tAUGUSTUS\tgene\t1\t5652\t0.46\t-\t.\tg1\r\n", "scaffold6_cov64\t2253\t2255\tscaffold6_cov64\tAUGUSTUS\tgene\t1\t5652\t0.46\t-\t.\tg1\r\n", "scaffold6_cov64\t2676\t2678\tscaffold6_cov64\tAUGUSTUS\tgene\t1\t5652\t0.46\t-\t.\tg1\r\n", "scaffold6_cov64\t2682\t2684\tscaffold6_cov64\tAUGUSTUS\tgene\t1\t5652\t0.46\t-\t.\tg1\r\n", "\r\n", "==> Meth3_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-Meth.bed-paGenes <==\r\n", "scaffold7_cov100\t7438\t7440\tscaffold7_cov100\tAUGUSTUS\tgene\t7069\t9073\t1\t-\t.\tg5\r\n", "scaffold7_cov100\t7696\t7698\tscaffold7_cov100\tAUGUSTUS\tgene\t7069\t9073\t1\t-\t.\tg5\r\n", "scaffold7_cov100\t7796\t7798\tscaffold7_cov100\tAUGUSTUS\tgene\t7069\t9073\t1\t-\t.\tg5\r\n", "scaffold7_cov100\t9877\t9879\tscaffold7_cov100\tAUGUSTUS\tgene\t9590\t11670\t0.8\t-\t.\tg6\r\n", "scaffold7_cov100\t10273\t10275\tscaffold7_cov100\tAUGUSTUS\tgene\t9590\t11670\t0.8\t-\t.\tg6\r\n", "scaffold7_cov100\t11043\t11045\tscaffold7_cov100\tAUGUSTUS\tgene\t9590\t11670\t0.8\t-\t.\tg6\r\n", "scaffold7_cov100\t13385\t13387\tscaffold7_cov100\tAUGUSTUS\tgene\t13339\t15463\t0.92\t-\t.\tg7\r\n", "scaffold7_cov100\t17527\t17529\tscaffold7_cov100\tAUGUSTUS\tgene\t15738\t18320\t0.96\t+\t.\tg8\r\n", "scaffold7_cov100\t17552\t17554\tscaffold7_cov100\tAUGUSTUS\tgene\t15738\t18320\t0.96\t+\t.\tg8\r\n", "scaffold7_cov100\t17633\t17635\tscaffold7_cov100\tAUGUSTUS\tgene\t15738\t18320\t0.96\t+\t.\tg8\r\n", "\r\n", "==> Meth3_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-sparseMeth.bed-paGenes <==\r\n", "scaffold7_cov100\t4630\t4632\tscaffold7_cov100\tAUGUSTUS\tgene\t3467\t6217\t0.78\t-\t.\tg4\r\n", "scaffold7_cov100\t4678\t4680\tscaffold7_cov100\tAUGUSTUS\tgene\t3467\t6217\t0.78\t-\t.\tg4\r\n", "scaffold7_cov100\t9715\t9717\tscaffold7_cov100\tAUGUSTUS\tgene\t9590\t11670\t0.8\t-\t.\tg6\r\n", "scaffold7_cov100\t11439\t11441\tscaffold7_cov100\tAUGUSTUS\tgene\t9590\t11670\t0.8\t-\t.\tg6\r\n", "scaffold7_cov100\t13450\t13452\tscaffold7_cov100\tAUGUSTUS\tgene\t13339\t15463\t0.92\t-\t.\tg7\r\n", "scaffold7_cov100\t17212\t17214\tscaffold7_cov100\tAUGUSTUS\tgene\t15738\t18320\t0.96\t+\t.\tg8\r\n", "scaffold7_cov100\t17952\t17954\tscaffold7_cov100\tAUGUSTUS\tgene\t15738\t18320\t0.96\t+\t.\tg8\r\n", "scaffold7_cov100\t20473\t20475\tscaffold7_cov100\tAUGUSTUS\tgene\t20078\t24295\t0.39\t+\t.\tg11\r\n", "scaffold7_cov100\t29397\t29399\tscaffold7_cov100\tAUGUSTUS\tgene\t28517\t29779\t0.69\t-\t.\tg12\r\n", "scaffold7_cov100\t41722\t41724\tscaffold7_cov100\tAUGUSTUS\tgene\t41188\t47537\t0.97\t+\t.\tg14\r\n", "\r\n", "==> Meth3_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-unMeth.bed-paGenes <==\r\n", "scaffold6_cov64\t290\t292\tscaffold6_cov64\tAUGUSTUS\tgene\t1\t5652\t0.46\t-\t.\tg1\r\n", "scaffold6_cov64\t298\t300\tscaffold6_cov64\tAUGUSTUS\tgene\t1\t5652\t0.46\t-\t.\tg1\r\n", "scaffold6_cov64\t489\t491\tscaffold6_cov64\tAUGUSTUS\tgene\t1\t5652\t0.46\t-\t.\tg1\r\n", "scaffold6_cov64\t826\t828\tscaffold6_cov64\tAUGUSTUS\tgene\t1\t5652\t0.46\t-\t.\tg1\r\n", "scaffold6_cov64\t2179\t2181\tscaffold6_cov64\tAUGUSTUS\tgene\t1\t5652\t0.46\t-\t.\tg1\r\n", "scaffold6_cov64\t2676\t2678\tscaffold6_cov64\tAUGUSTUS\tgene\t1\t5652\t0.46\t-\t.\tg1\r\n", "scaffold6_cov64\t2682\t2684\tscaffold6_cov64\tAUGUSTUS\tgene\t1\t5652\t0.46\t-\t.\tg1\r\n", "scaffold6_cov64\t2805\t2807\tscaffold6_cov64\tAUGUSTUS\tgene\t1\t5652\t0.46\t-\t.\tg1\r\n", "scaffold6_cov64\t2876\t2878\tscaffold6_cov64\tAUGUSTUS\tgene\t1\t5652\t0.46\t-\t.\tg1\r\n", "scaffold6_cov64\t3054\t3056\tscaffold6_cov64\tAUGUSTUS\tgene\t1\t5652\t0.46\t-\t.\tg1\r\n", "\r\n", "==> Meth3_R1_001_val_1_bismark_bt2_pe._10x.bedgraph.bed-paGenes <==\r\n", "scaffold6_cov64\t290\t292\tscaffold6_cov64\tAUGUSTUS\tgene\t1\t5652\t0.46\t-\t.\tg1\r\n", "scaffold6_cov64\t298\t300\tscaffold6_cov64\tAUGUSTUS\tgene\t1\t5652\t0.46\t-\t.\tg1\r\n", "scaffold6_cov64\t489\t491\tscaffold6_cov64\tAUGUSTUS\tgene\t1\t5652\t0.46\t-\t.\tg1\r\n", "scaffold6_cov64\t826\t828\tscaffold6_cov64\tAUGUSTUS\tgene\t1\t5652\t0.46\t-\t.\tg1\r\n", "scaffold6_cov64\t2179\t2181\tscaffold6_cov64\tAUGUSTUS\tgene\t1\t5652\t0.46\t-\t.\tg1\r\n", "scaffold6_cov64\t2676\t2678\tscaffold6_cov64\tAUGUSTUS\tgene\t1\t5652\t0.46\t-\t.\tg1\r\n", "scaffold6_cov64\t2682\t2684\tscaffold6_cov64\tAUGUSTUS\tgene\t1\t5652\t0.46\t-\t.\tg1\r\n", "scaffold6_cov64\t2805\t2807\tscaffold6_cov64\tAUGUSTUS\tgene\t1\t5652\t0.46\t-\t.\tg1\r\n", "scaffold6_cov64\t2876\t2878\tscaffold6_cov64\tAUGUSTUS\tgene\t1\t5652\t0.46\t-\t.\tg1\r\n", "scaffold6_cov64\t3054\t3056\tscaffold6_cov64\tAUGUSTUS\tgene\t1\t5652\t0.46\t-\t.\tg1\r\n", "\r\n", "==> Meth4_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-Meth.bed-paGenes <==\r\n", "scaffold7_cov100\t96791\t96793\tscaffold7_cov100\tAUGUSTUS\tgene\t92374\t98904\t0.33\t-\t.\tg24\r\n", "scaffold7_cov100\t109716\t109718\tscaffold7_cov100\tAUGUSTUS\tgene\t109033\t116378\t0.55\t+\t.\tg28\r\n", "scaffold7_cov100\t338971\t338973\tscaffold7_cov100\tAUGUSTUS\tgene\t335162\t340237\t0.67\t+\t.\tg74\r\n", "scaffold7_cov100\t360165\t360167\tscaffold7_cov100\tAUGUSTUS\tgene\t357089\t366361\t0.39\t-\t.\tg79\r\n", "scaffold7_cov100\t394699\t394701\tscaffold7_cov100\tAUGUSTUS\tgene\t391997\t395438\t0.56\t-\t.\tg86\r\n", "scaffold7_cov100\t403347\t403349\tscaffold7_cov100\tAUGUSTUS\tgene\t400953\t405275\t0.29\t+\t.\tg87\r\n", "scaffold7_cov100\t403727\t403729\tscaffold7_cov100\tAUGUSTUS\tgene\t400953\t405275\t0.29\t+\t.\tg87\r\n", "scaffold7_cov100\t440492\t440494\tscaffold7_cov100\tAUGUSTUS\tgene\t433402\t442117\t0.39\t-\t.\tg94\r\n", "scaffold7_cov100\t440575\t440577\tscaffold7_cov100\tAUGUSTUS\tgene\t433402\t442117\t0.39\t-\t.\tg94\r\n", "scaffold7_cov100\t440593\t440595\tscaffold7_cov100\tAUGUSTUS\tgene\t433402\t442117\t0.39\t-\t.\tg94\r\n", "\r\n", "==> Meth4_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-sparseMeth.bed-paGenes <==\r\n", "scaffold6_cov64\t5904\t5906\tscaffold6_cov64\tAUGUSTUS\tgene\t5805\t6678\t0.57\t+\t.\tg2\r\n", "scaffold7_cov100\t4351\t4353\tscaffold7_cov100\tAUGUSTUS\tgene\t3467\t6217\t0.78\t-\t.\tg4\r\n", "scaffold7_cov100\t46343\t46345\tscaffold7_cov100\tAUGUSTUS\tgene\t41188\t47537\t0.97\t+\t.\tg14\r\n", "scaffold7_cov100\t46397\t46399\tscaffold7_cov100\tAUGUSTUS\tgene\t41188\t47537\t0.97\t+\t.\tg14\r\n", "scaffold7_cov100\t55479\t55481\tscaffold7_cov100\tAUGUSTUS\tgene\t50051\t63721\t1\t+\t.\tg16\r\n", "scaffold7_cov100\t61080\t61082\tscaffold7_cov100\tAUGUSTUS\tgene\t50051\t63721\t1\t+\t.\tg16\r\n", "scaffold7_cov100\t81500\t81502\tscaffold7_cov100\tAUGUSTUS\tgene\t80104\t82819\t1\t-\t.\tg22\r\n", "scaffold7_cov100\t91941\t91943\tscaffold7_cov100\tAUGUSTUS\tgene\t87978\t91989\t0.37\t-\t.\tg23\r\n", "scaffold7_cov100\t96787\t96789\tscaffold7_cov100\tAUGUSTUS\tgene\t92374\t98904\t0.33\t-\t.\tg24\r\n", "scaffold7_cov100\t115927\t115929\tscaffold7_cov100\tAUGUSTUS\tgene\t109033\t116378\t0.55\t+\t.\tg28\r\n", "\r\n", "==> Meth4_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-unMeth.bed-paGenes <==\r\n", "scaffold6_cov64\t5456\t5458\tscaffold6_cov64\tAUGUSTUS\tgene\t1\t5652\t0.46\t-\t.\tg1\r\n", "scaffold6_cov64\t5486\t5488\tscaffold6_cov64\tAUGUSTUS\tgene\t1\t5652\t0.46\t-\t.\tg1\r\n", "scaffold6_cov64\t5545\t5547\tscaffold6_cov64\tAUGUSTUS\tgene\t1\t5652\t0.46\t-\t.\tg1\r\n", "scaffold6_cov64\t5559\t5561\tscaffold6_cov64\tAUGUSTUS\tgene\t1\t5652\t0.46\t-\t.\tg1\r\n", "scaffold6_cov64\t5561\t5563\tscaffold6_cov64\tAUGUSTUS\tgene\t1\t5652\t0.46\t-\t.\tg1\r\n", "scaffold6_cov64\t5567\t5569\tscaffold6_cov64\tAUGUSTUS\tgene\t1\t5652\t0.46\t-\t.\tg1\r\n", "scaffold6_cov64\t5574\t5576\tscaffold6_cov64\tAUGUSTUS\tgene\t1\t5652\t0.46\t-\t.\tg1\r\n", "scaffold6_cov64\t5581\t5583\tscaffold6_cov64\tAUGUSTUS\tgene\t1\t5652\t0.46\t-\t.\tg1\r\n", "scaffold6_cov64\t5583\t5585\tscaffold6_cov64\tAUGUSTUS\tgene\t1\t5652\t0.46\t-\t.\tg1\r\n", "scaffold6_cov64\t5592\t5594\tscaffold6_cov64\tAUGUSTUS\tgene\t1\t5652\t0.46\t-\t.\tg1\r\n", "\r\n", "==> Meth4_R1_001_val_1_bismark_bt2_pe._10x.bedgraph.bed-paGenes <==\r\n", "scaffold6_cov64\t5456\t5458\tscaffold6_cov64\tAUGUSTUS\tgene\t1\t5652\t0.46\t-\t.\tg1\r\n", "scaffold6_cov64\t5486\t5488\tscaffold6_cov64\tAUGUSTUS\tgene\t1\t5652\t0.46\t-\t.\tg1\r\n", "scaffold6_cov64\t5545\t5547\tscaffold6_cov64\tAUGUSTUS\tgene\t1\t5652\t0.46\t-\t.\tg1\r\n", "scaffold6_cov64\t5559\t5561\tscaffold6_cov64\tAUGUSTUS\tgene\t1\t5652\t0.46\t-\t.\tg1\r\n", "scaffold6_cov64\t5561\t5563\tscaffold6_cov64\tAUGUSTUS\tgene\t1\t5652\t0.46\t-\t.\tg1\r\n", "scaffold6_cov64\t5567\t5569\tscaffold6_cov64\tAUGUSTUS\tgene\t1\t5652\t0.46\t-\t.\tg1\r\n", "scaffold6_cov64\t5574\t5576\tscaffold6_cov64\tAUGUSTUS\tgene\t1\t5652\t0.46\t-\t.\tg1\r\n", "scaffold6_cov64\t5581\t5583\tscaffold6_cov64\tAUGUSTUS\tgene\t1\t5652\t0.46\t-\t.\tg1\r\n", "scaffold6_cov64\t5583\t5585\tscaffold6_cov64\tAUGUSTUS\tgene\t1\t5652\t0.46\t-\t.\tg1\r\n", "scaffold6_cov64\t5592\t5594\tscaffold6_cov64\tAUGUSTUS\tgene\t1\t5652\t0.46\t-\t.\tg1\r\n", "\r\n", "==> Meth5_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-Meth.bed-paGenes <==\r\n", "scaffold7_cov100\t61080\t61082\tscaffold7_cov100\tAUGUSTUS\tgene\t50051\t63721\t1\t+\t.\tg16\r\n", "scaffold7_cov100\t96787\t96789\tscaffold7_cov100\tAUGUSTUS\tgene\t92374\t98904\t0.33\t-\t.\tg24\r\n", "scaffold7_cov100\t96791\t96793\tscaffold7_cov100\tAUGUSTUS\tgene\t92374\t98904\t0.33\t-\t.\tg24\r\n", "scaffold7_cov100\t96859\t96861\tscaffold7_cov100\tAUGUSTUS\tgene\t92374\t98904\t0.33\t-\t.\tg24\r\n", "scaffold7_cov100\t177834\t177836\tscaffold7_cov100\tAUGUSTUS\tgene\t169668\t186287\t0.65\t-\t.\tg44\r\n", "scaffold7_cov100\t177838\t177840\tscaffold7_cov100\tAUGUSTUS\tgene\t169668\t186287\t0.65\t-\t.\tg44\r\n", "scaffold7_cov100\t204124\t204126\tscaffold7_cov100\tAUGUSTUS\tgene\t199926\t204500\t0.34\t-\t.\tg47\r\n", "scaffold7_cov100\t253591\t253593\tscaffold7_cov100\tAUGUSTUS\tgene\t252179\t254141\t0.9\t-\t.\tg53\r\n", "scaffold7_cov100\t338971\t338973\tscaffold7_cov100\tAUGUSTUS\tgene\t335162\t340237\t0.67\t+\t.\tg74\r\n", "scaffold7_cov100\t346786\t346788\tscaffold7_cov100\tAUGUSTUS\tgene\t346473\t355075\t0.09\t+\t.\tg78\r\n", "\r\n", "==> Meth5_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-sparseMeth.bed-paGenes <==\r\n", "scaffold6_cov64\t6374\t6376\tscaffold6_cov64\tAUGUSTUS\tgene\t5805\t6678\t0.57\t+\t.\tg2\r\n", "scaffold7_cov100\t46343\t46345\tscaffold7_cov100\tAUGUSTUS\tgene\t41188\t47537\t0.97\t+\t.\tg14\r\n", "scaffold7_cov100\t94139\t94141\tscaffold7_cov100\tAUGUSTUS\tgene\t92374\t98904\t0.33\t-\t.\tg24\r\n", "scaffold7_cov100\t94142\t94144\tscaffold7_cov100\tAUGUSTUS\tgene\t92374\t98904\t0.33\t-\t.\tg24\r\n", "scaffold7_cov100\t94939\t94941\tscaffold7_cov100\tAUGUSTUS\tgene\t92374\t98904\t0.33\t-\t.\tg24\r\n", "scaffold7_cov100\t131174\t131176\tscaffold7_cov100\tAUGUSTUS\tgene\t121645\t131291\t0.02\t+\t.\tg31\r\n", "scaffold7_cov100\t177836\t177838\tscaffold7_cov100\tAUGUSTUS\tgene\t169668\t186287\t0.65\t-\t.\tg44\r\n", "scaffold7_cov100\t236368\t236370\tscaffold7_cov100\tAUGUSTUS\tgene\t235762\t238228\t0.38\t-\t.\tg51\r\n", "scaffold7_cov100\t386815\t386817\tscaffold7_cov100\tAUGUSTUS\tgene\t386292\t387086\t0.59\t+\t.\tg84\r\n", "scaffold7_cov100\t404820\t404822\tscaffold7_cov100\tAUGUSTUS\tgene\t400953\t405275\t0.29\t+\t.\tg87\r\n", "\r\n", "==> Meth5_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-unMeth.bed-paGenes <==\r\n", "scaffold6_cov64\t4588\t4590\tscaffold6_cov64\tAUGUSTUS\tgene\t1\t5652\t0.46\t-\t.\tg1\r\n", "scaffold6_cov64\t5559\t5561\tscaffold6_cov64\tAUGUSTUS\tgene\t1\t5652\t0.46\t-\t.\tg1\r\n", "scaffold6_cov64\t5561\t5563\tscaffold6_cov64\tAUGUSTUS\tgene\t1\t5652\t0.46\t-\t.\tg1\r\n", "scaffold6_cov64\t5567\t5569\tscaffold6_cov64\tAUGUSTUS\tgene\t1\t5652\t0.46\t-\t.\tg1\r\n", "scaffold6_cov64\t5574\t5576\tscaffold6_cov64\tAUGUSTUS\tgene\t1\t5652\t0.46\t-\t.\tg1\r\n", "scaffold6_cov64\t5581\t5583\tscaffold6_cov64\tAUGUSTUS\tgene\t1\t5652\t0.46\t-\t.\tg1\r\n", "scaffold6_cov64\t5583\t5585\tscaffold6_cov64\tAUGUSTUS\tgene\t1\t5652\t0.46\t-\t.\tg1\r\n", "scaffold6_cov64\t5592\t5594\tscaffold6_cov64\tAUGUSTUS\tgene\t1\t5652\t0.46\t-\t.\tg1\r\n", "scaffold6_cov64\t5594\t5596\tscaffold6_cov64\tAUGUSTUS\tgene\t1\t5652\t0.46\t-\t.\tg1\r\n", "scaffold6_cov64\t5604\t5606\tscaffold6_cov64\tAUGUSTUS\tgene\t1\t5652\t0.46\t-\t.\tg1\r\n", "\r\n", "==> Meth5_R1_001_val_1_bismark_bt2_pe._10x.bedgraph.bed-paGenes <==\r\n", "scaffold6_cov64\t4588\t4590\tscaffold6_cov64\tAUGUSTUS\tgene\t1\t5652\t0.46\t-\t.\tg1\r\n", "scaffold6_cov64\t5559\t5561\tscaffold6_cov64\tAUGUSTUS\tgene\t1\t5652\t0.46\t-\t.\tg1\r\n", "scaffold6_cov64\t5561\t5563\tscaffold6_cov64\tAUGUSTUS\tgene\t1\t5652\t0.46\t-\t.\tg1\r\n", "scaffold6_cov64\t5567\t5569\tscaffold6_cov64\tAUGUSTUS\tgene\t1\t5652\t0.46\t-\t.\tg1\r\n", "scaffold6_cov64\t5574\t5576\tscaffold6_cov64\tAUGUSTUS\tgene\t1\t5652\t0.46\t-\t.\tg1\r\n", "scaffold6_cov64\t5581\t5583\tscaffold6_cov64\tAUGUSTUS\tgene\t1\t5652\t0.46\t-\t.\tg1\r\n", "scaffold6_cov64\t5583\t5585\tscaffold6_cov64\tAUGUSTUS\tgene\t1\t5652\t0.46\t-\t.\tg1\r\n", "scaffold6_cov64\t5592\t5594\tscaffold6_cov64\tAUGUSTUS\tgene\t1\t5652\t0.46\t-\t.\tg1\r\n", "scaffold6_cov64\t5594\t5596\tscaffold6_cov64\tAUGUSTUS\tgene\t1\t5652\t0.46\t-\t.\tg1\r\n", "scaffold6_cov64\t5604\t5606\tscaffold6_cov64\tAUGUSTUS\tgene\t1\t5652\t0.46\t-\t.\tg1\r\n", "\r\n", "==> Meth6_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-Meth.bed-paGenes <==\r\n", "scaffold7_cov100\t346786\t346788\tscaffold7_cov100\tAUGUSTUS\tgene\t346473\t355075\t0.09\t+\t.\tg78\r\n", "scaffold7_cov100\t360165\t360167\tscaffold7_cov100\tAUGUSTUS\tgene\t357089\t366361\t0.39\t-\t.\tg79\r\n", "scaffold7_cov100\t386815\t386817\tscaffold7_cov100\tAUGUSTUS\tgene\t386292\t387086\t0.59\t+\t.\tg84\r\n", "scaffold7_cov100\t386817\t386819\tscaffold7_cov100\tAUGUSTUS\tgene\t386292\t387086\t0.59\t+\t.\tg84\r\n", "scaffold7_cov100\t394699\t394701\tscaffold7_cov100\tAUGUSTUS\tgene\t391997\t395438\t0.56\t-\t.\tg86\r\n", "scaffold7_cov100\t403347\t403349\tscaffold7_cov100\tAUGUSTUS\tgene\t400953\t405275\t0.29\t+\t.\tg87\r\n", "scaffold7_cov100\t403727\t403729\tscaffold7_cov100\tAUGUSTUS\tgene\t400953\t405275\t0.29\t+\t.\tg87\r\n", "scaffold7_cov100\t426679\t426681\tscaffold7_cov100\tAUGUSTUS\tgene\t420923\t432336\t0.45\t-\t.\tg91\r\n", "scaffold7_cov100\t440492\t440494\tscaffold7_cov100\tAUGUSTUS\tgene\t433402\t442117\t0.39\t-\t.\tg94\r\n", "scaffold7_cov100\t440575\t440577\tscaffold7_cov100\tAUGUSTUS\tgene\t433402\t442117\t0.39\t-\t.\tg94\r\n", "\r\n", "==> Meth6_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-sparseMeth.bed-paGenes <==\r\n", "scaffold6_cov64\t5604\t5606\tscaffold6_cov64\tAUGUSTUS\tgene\t1\t5652\t0.46\t-\t.\tg1\r\n", "scaffold6_cov64\t6266\t6268\tscaffold6_cov64\tAUGUSTUS\tgene\t5805\t6678\t0.57\t+\t.\tg2\r\n", "scaffold7_cov100\t4351\t4353\tscaffold7_cov100\tAUGUSTUS\tgene\t3467\t6217\t0.78\t-\t.\tg4\r\n", "scaffold7_cov100\t32521\t32523\tscaffold7_cov100\tAUGUSTUS\tgene\t31898\t37761\t0.64\t-\t.\tg13\r\n", "scaffold7_cov100\t32984\t32986\tscaffold7_cov100\tAUGUSTUS\tgene\t31898\t37761\t0.64\t-\t.\tg13\r\n", "scaffold7_cov100\t46343\t46345\tscaffold7_cov100\tAUGUSTUS\tgene\t41188\t47537\t0.97\t+\t.\tg14\r\n", "scaffold7_cov100\t61080\t61082\tscaffold7_cov100\tAUGUSTUS\tgene\t50051\t63721\t1\t+\t.\tg16\r\n", "scaffold7_cov100\t82753\t82755\tscaffold7_cov100\tAUGUSTUS\tgene\t80104\t82819\t1\t-\t.\tg22\r\n", "scaffold7_cov100\t109704\t109706\tscaffold7_cov100\tAUGUSTUS\tgene\t109033\t116378\t0.55\t+\t.\tg28\r\n", "scaffold7_cov100\t109716\t109718\tscaffold7_cov100\tAUGUSTUS\tgene\t109033\t116378\t0.55\t+\t.\tg28\r\n", "\r\n", "==> Meth6_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-unMeth.bed-paGenes <==\r\n", "scaffold6_cov64\t5545\t5547\tscaffold6_cov64\tAUGUSTUS\tgene\t1\t5652\t0.46\t-\t.\tg1\r\n", "scaffold6_cov64\t5559\t5561\tscaffold6_cov64\tAUGUSTUS\tgene\t1\t5652\t0.46\t-\t.\tg1\r\n", "scaffold6_cov64\t5561\t5563\tscaffold6_cov64\tAUGUSTUS\tgene\t1\t5652\t0.46\t-\t.\tg1\r\n", "scaffold6_cov64\t5567\t5569\tscaffold6_cov64\tAUGUSTUS\tgene\t1\t5652\t0.46\t-\t.\tg1\r\n", "scaffold6_cov64\t5574\t5576\tscaffold6_cov64\tAUGUSTUS\tgene\t1\t5652\t0.46\t-\t.\tg1\r\n", "scaffold6_cov64\t5581\t5583\tscaffold6_cov64\tAUGUSTUS\tgene\t1\t5652\t0.46\t-\t.\tg1\r\n", "scaffold6_cov64\t5583\t5585\tscaffold6_cov64\tAUGUSTUS\tgene\t1\t5652\t0.46\t-\t.\tg1\r\n", "scaffold6_cov64\t5592\t5594\tscaffold6_cov64\tAUGUSTUS\tgene\t1\t5652\t0.46\t-\t.\tg1\r\n", "scaffold6_cov64\t5594\t5596\tscaffold6_cov64\tAUGUSTUS\tgene\t1\t5652\t0.46\t-\t.\tg1\r\n", "scaffold6_cov64\t5644\t5646\tscaffold6_cov64\tAUGUSTUS\tgene\t1\t5652\t0.46\t-\t.\tg1\r\n", "\r\n", "==> Meth6_R1_001_val_1_bismark_bt2_pe._10x.bedgraph.bed-paGenes <==\r\n", "scaffold6_cov64\t5545\t5547\tscaffold6_cov64\tAUGUSTUS\tgene\t1\t5652\t0.46\t-\t.\tg1\r\n", "scaffold6_cov64\t5559\t5561\tscaffold6_cov64\tAUGUSTUS\tgene\t1\t5652\t0.46\t-\t.\tg1\r\n", "scaffold6_cov64\t5561\t5563\tscaffold6_cov64\tAUGUSTUS\tgene\t1\t5652\t0.46\t-\t.\tg1\r\n", "scaffold6_cov64\t5567\t5569\tscaffold6_cov64\tAUGUSTUS\tgene\t1\t5652\t0.46\t-\t.\tg1\r\n", "scaffold6_cov64\t5574\t5576\tscaffold6_cov64\tAUGUSTUS\tgene\t1\t5652\t0.46\t-\t.\tg1\r\n", "scaffold6_cov64\t5581\t5583\tscaffold6_cov64\tAUGUSTUS\tgene\t1\t5652\t0.46\t-\t.\tg1\r\n", "scaffold6_cov64\t5583\t5585\tscaffold6_cov64\tAUGUSTUS\tgene\t1\t5652\t0.46\t-\t.\tg1\r\n", "scaffold6_cov64\t5592\t5594\tscaffold6_cov64\tAUGUSTUS\tgene\t1\t5652\t0.46\t-\t.\tg1\r\n", "scaffold6_cov64\t5594\t5596\tscaffold6_cov64\tAUGUSTUS\tgene\t1\t5652\t0.46\t-\t.\tg1\r\n", "scaffold6_cov64\t5604\t5606\tscaffold6_cov64\tAUGUSTUS\tgene\t1\t5652\t0.46\t-\t.\tg1\r\n", "\r\n", "==> Meth7_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-Meth.bed-paGenes <==\r\n", "scaffold7_cov100\t5500\t5502\tscaffold7_cov100\tAUGUSTUS\tgene\t3467\t6217\t0.78\t-\t.\tg4\r\n", "scaffold7_cov100\t5986\t5988\tscaffold7_cov100\tAUGUSTUS\tgene\t3467\t6217\t0.78\t-\t.\tg4\r\n", "scaffold7_cov100\t6144\t6146\tscaffold7_cov100\tAUGUSTUS\tgene\t3467\t6217\t0.78\t-\t.\tg4\r\n", "scaffold7_cov100\t6188\t6190\tscaffold7_cov100\tAUGUSTUS\tgene\t3467\t6217\t0.78\t-\t.\tg4\r\n", "scaffold7_cov100\t6198\t6200\tscaffold7_cov100\tAUGUSTUS\tgene\t3467\t6217\t0.78\t-\t.\tg4\r\n", "scaffold7_cov100\t7438\t7440\tscaffold7_cov100\tAUGUSTUS\tgene\t7069\t9073\t1\t-\t.\tg5\r\n", "scaffold7_cov100\t7696\t7698\tscaffold7_cov100\tAUGUSTUS\tgene\t7069\t9073\t1\t-\t.\tg5\r\n", "scaffold7_cov100\t7796\t7798\tscaffold7_cov100\tAUGUSTUS\tgene\t7069\t9073\t1\t-\t.\tg5\r\n", "scaffold7_cov100\t7891\t7893\tscaffold7_cov100\tAUGUSTUS\tgene\t7069\t9073\t1\t-\t.\tg5\r\n", "scaffold7_cov100\t9877\t9879\tscaffold7_cov100\tAUGUSTUS\tgene\t9590\t11670\t0.8\t-\t.\tg6\r\n", "\r\n", "==> Meth7_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-sparseMeth.bed-paGenes <==\r\n", "scaffold7_cov100\t2080\t2082\tscaffold7_cov100\tAUGUSTUS\tgene\t1\t2566\t0.96\t+\t.\tg3\r\n", "scaffold7_cov100\t11439\t11441\tscaffold7_cov100\tAUGUSTUS\tgene\t9590\t11670\t0.8\t-\t.\tg6\r\n", "scaffold7_cov100\t14042\t14044\tscaffold7_cov100\tAUGUSTUS\tgene\t13339\t15463\t0.92\t-\t.\tg7\r\n", "scaffold7_cov100\t17952\t17954\tscaffold7_cov100\tAUGUSTUS\tgene\t15738\t18320\t0.96\t+\t.\tg8\r\n", "scaffold7_cov100\t19493\t19495\tscaffold7_cov100\tAUGUSTUS\tgene\t19312\t20050\t0.74\t+\t.\tg10\r\n", "scaffold7_cov100\t52752\t52754\tscaffold7_cov100\tAUGUSTUS\tgene\t50051\t63721\t1\t+\t.\tg16\r\n", "scaffold7_cov100\t52903\t52905\tscaffold7_cov100\tAUGUSTUS\tgene\t50051\t63721\t1\t+\t.\tg16\r\n", "scaffold7_cov100\t66986\t66988\tscaffold7_cov100\tAUGUSTUS\tgene\t65053\t67396\t1\t-\t.\tg17\r\n", "scaffold7_cov100\t68605\t68607\tscaffold7_cov100\tAUGUSTUS\tgene\t68185\t73140\t1\t-\t.\tg18\r\n", "scaffold7_cov100\t69313\t69315\tscaffold7_cov100\tAUGUSTUS\tgene\t68185\t73140\t1\t-\t.\tg18\r\n", "\r\n", "==> Meth7_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-unMeth.bed-paGenes <==\r\n", "scaffold6_cov64\t489\t491\tscaffold6_cov64\tAUGUSTUS\tgene\t1\t5652\t0.46\t-\t.\tg1\r\n", "scaffold6_cov64\t3343\t3345\tscaffold6_cov64\tAUGUSTUS\tgene\t1\t5652\t0.46\t-\t.\tg1\r\n", "scaffold6_cov64\t3420\t3422\tscaffold6_cov64\tAUGUSTUS\tgene\t1\t5652\t0.46\t-\t.\tg1\r\n", "scaffold6_cov64\t3435\t3437\tscaffold6_cov64\tAUGUSTUS\tgene\t1\t5652\t0.46\t-\t.\tg1\r\n", "scaffold6_cov64\t3439\t3441\tscaffold6_cov64\tAUGUSTUS\tgene\t1\t5652\t0.46\t-\t.\tg1\r\n", "scaffold6_cov64\t3444\t3446\tscaffold6_cov64\tAUGUSTUS\tgene\t1\t5652\t0.46\t-\t.\tg1\r\n", "scaffold6_cov64\t3507\t3509\tscaffold6_cov64\tAUGUSTUS\tgene\t1\t5652\t0.46\t-\t.\tg1\r\n", "scaffold6_cov64\t3569\t3571\tscaffold6_cov64\tAUGUSTUS\tgene\t1\t5652\t0.46\t-\t.\tg1\r\n", "scaffold6_cov64\t3596\t3598\tscaffold6_cov64\tAUGUSTUS\tgene\t1\t5652\t0.46\t-\t.\tg1\r\n", "scaffold6_cov64\t5266\t5268\tscaffold6_cov64\tAUGUSTUS\tgene\t1\t5652\t0.46\t-\t.\tg1\r\n", "\r\n", "==> Meth7_R1_001_val_1_bismark_bt2_pe._10x.bedgraph.bed-paGenes <==\r\n", "scaffold6_cov64\t489\t491\tscaffold6_cov64\tAUGUSTUS\tgene\t1\t5652\t0.46\t-\t.\tg1\r\n", "scaffold6_cov64\t3343\t3345\tscaffold6_cov64\tAUGUSTUS\tgene\t1\t5652\t0.46\t-\t.\tg1\r\n", "scaffold6_cov64\t3420\t3422\tscaffold6_cov64\tAUGUSTUS\tgene\t1\t5652\t0.46\t-\t.\tg1\r\n", "scaffold6_cov64\t3435\t3437\tscaffold6_cov64\tAUGUSTUS\tgene\t1\t5652\t0.46\t-\t.\tg1\r\n", "scaffold6_cov64\t3439\t3441\tscaffold6_cov64\tAUGUSTUS\tgene\t1\t5652\t0.46\t-\t.\tg1\r\n", "scaffold6_cov64\t3444\t3446\tscaffold6_cov64\tAUGUSTUS\tgene\t1\t5652\t0.46\t-\t.\tg1\r\n", "scaffold6_cov64\t3507\t3509\tscaffold6_cov64\tAUGUSTUS\tgene\t1\t5652\t0.46\t-\t.\tg1\r\n", "scaffold6_cov64\t3569\t3571\tscaffold6_cov64\tAUGUSTUS\tgene\t1\t5652\t0.46\t-\t.\tg1\r\n", "scaffold6_cov64\t3596\t3598\tscaffold6_cov64\tAUGUSTUS\tgene\t1\t5652\t0.46\t-\t.\tg1\r\n", "scaffold6_cov64\t5266\t5268\tscaffold6_cov64\tAUGUSTUS\tgene\t1\t5652\t0.46\t-\t.\tg1\r\n", "\r\n", "==> Meth8_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-Meth.bed-paGenes <==\r\n", "scaffold7_cov100\t5986\t5988\tscaffold7_cov100\tAUGUSTUS\tgene\t3467\t6217\t0.78\t-\t.\tg4\r\n", "scaffold7_cov100\t6144\t6146\tscaffold7_cov100\tAUGUSTUS\tgene\t3467\t6217\t0.78\t-\t.\tg4\r\n", "scaffold7_cov100\t6188\t6190\tscaffold7_cov100\tAUGUSTUS\tgene\t3467\t6217\t0.78\t-\t.\tg4\r\n", "scaffold7_cov100\t6198\t6200\tscaffold7_cov100\tAUGUSTUS\tgene\t3467\t6217\t0.78\t-\t.\tg4\r\n", "scaffold7_cov100\t7796\t7798\tscaffold7_cov100\tAUGUSTUS\tgene\t7069\t9073\t1\t-\t.\tg5\r\n", "scaffold7_cov100\t7891\t7893\tscaffold7_cov100\tAUGUSTUS\tgene\t7069\t9073\t1\t-\t.\tg5\r\n", "scaffold7_cov100\t16831\t16833\tscaffold7_cov100\tAUGUSTUS\tgene\t15738\t18320\t0.96\t+\t.\tg8\r\n", "scaffold7_cov100\t16910\t16912\tscaffold7_cov100\tAUGUSTUS\tgene\t15738\t18320\t0.96\t+\t.\tg8\r\n", "scaffold7_cov100\t16940\t16942\tscaffold7_cov100\tAUGUSTUS\tgene\t15738\t18320\t0.96\t+\t.\tg8\r\n", "scaffold7_cov100\t17000\t17002\tscaffold7_cov100\tAUGUSTUS\tgene\t15738\t18320\t0.96\t+\t.\tg8\r\n", "\r\n", "==> Meth8_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-sparseMeth.bed-paGenes <==\r\n", "scaffold7_cov100\t5500\t5502\tscaffold7_cov100\tAUGUSTUS\tgene\t3467\t6217\t0.78\t-\t.\tg4\r\n", "scaffold7_cov100\t13385\t13387\tscaffold7_cov100\tAUGUSTUS\tgene\t13339\t15463\t0.92\t-\t.\tg7\r\n", "scaffold7_cov100\t131221\t131223\tscaffold7_cov100\tAUGUSTUS\tgene\t121645\t131291\t0.02\t+\t.\tg31\r\n", "scaffold7_cov100\t131255\t131257\tscaffold7_cov100\tAUGUSTUS\tgene\t121645\t131291\t0.02\t+\t.\tg31\r\n", "scaffold7_cov100\t155682\t155684\tscaffold7_cov100\tAUGUSTUS\tgene\t152988\t156409\t0.36\t-\t.\tg41\r\n", "scaffold7_cov100\t470212\t470214\tscaffold7_cov100\tAUGUSTUS\tgene\t469917\t473613\t1\t+\t.\tg103\r\n", "scaffold7_cov100\t470966\t470968\tscaffold7_cov100\tAUGUSTUS\tgene\t469917\t473613\t1\t+\t.\tg103\r\n", "scaffold7_cov100\t471533\t471535\tscaffold7_cov100\tAUGUSTUS\tgene\t469917\t473613\t1\t+\t.\tg103\r\n", "scaffold19_cov103\t112974\t112976\tscaffold19_cov103\tAUGUSTUS\tgene\t112666\t114080\t0.55\t+\t.\tg169\r\n", "scaffold21_cov102\t86899\t86901\tscaffold21_cov102\tAUGUSTUS\tgene\t85557\t86981\t0.96\t+\t.\tg235\r\n", "\r\n", "==> Meth8_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-unMeth.bed-paGenes <==\r\n", "scaffold6_cov64\t6338\t6340\tscaffold6_cov64\tAUGUSTUS\tgene\t5805\t6678\t0.57\t+\t.\tg2\r\n", "scaffold6_cov64\t6344\t6346\tscaffold6_cov64\tAUGUSTUS\tgene\t5805\t6678\t0.57\t+\t.\tg2\r\n", "scaffold6_cov64\t6361\t6363\tscaffold6_cov64\tAUGUSTUS\tgene\t5805\t6678\t0.57\t+\t.\tg2\r\n", "scaffold6_cov64\t6374\t6376\tscaffold6_cov64\tAUGUSTUS\tgene\t5805\t6678\t0.57\t+\t.\tg2\r\n", "scaffold6_cov64\t6380\t6382\tscaffold6_cov64\tAUGUSTUS\tgene\t5805\t6678\t0.57\t+\t.\tg2\r\n", "scaffold6_cov64\t6387\t6389\tscaffold6_cov64\tAUGUSTUS\tgene\t5805\t6678\t0.57\t+\t.\tg2\r\n", "scaffold7_cov100\t5578\t5580\tscaffold7_cov100\tAUGUSTUS\tgene\t3467\t6217\t0.78\t-\t.\tg4\r\n", "scaffold7_cov100\t17164\t17166\tscaffold7_cov100\tAUGUSTUS\tgene\t15738\t18320\t0.96\t+\t.\tg8\r\n", "scaffold7_cov100\t46203\t46205\tscaffold7_cov100\tAUGUSTUS\tgene\t41188\t47537\t0.97\t+\t.\tg14\r\n", "scaffold7_cov100\t46206\t46208\tscaffold7_cov100\tAUGUSTUS\tgene\t41188\t47537\t0.97\t+\t.\tg14\r\n", "\r\n", "==> Meth8_R1_001_val_1_bismark_bt2_pe._10x.bedgraph.bed-paGenes <==\r\n", "scaffold6_cov64\t6338\t6340\tscaffold6_cov64\tAUGUSTUS\tgene\t5805\t6678\t0.57\t+\t.\tg2\r\n", "scaffold6_cov64\t6344\t6346\tscaffold6_cov64\tAUGUSTUS\tgene\t5805\t6678\t0.57\t+\t.\tg2\r\n", "scaffold6_cov64\t6361\t6363\tscaffold6_cov64\tAUGUSTUS\tgene\t5805\t6678\t0.57\t+\t.\tg2\r\n", "scaffold6_cov64\t6374\t6376\tscaffold6_cov64\tAUGUSTUS\tgene\t5805\t6678\t0.57\t+\t.\tg2\r\n", "scaffold6_cov64\t6380\t6382\tscaffold6_cov64\tAUGUSTUS\tgene\t5805\t6678\t0.57\t+\t.\tg2\r\n", "scaffold6_cov64\t6387\t6389\tscaffold6_cov64\tAUGUSTUS\tgene\t5805\t6678\t0.57\t+\t.\tg2\r\n", "scaffold7_cov100\t5500\t5502\tscaffold7_cov100\tAUGUSTUS\tgene\t3467\t6217\t0.78\t-\t.\tg4\r\n", "scaffold7_cov100\t5578\t5580\tscaffold7_cov100\tAUGUSTUS\tgene\t3467\t6217\t0.78\t-\t.\tg4\r\n", "scaffold7_cov100\t5986\t5988\tscaffold7_cov100\tAUGUSTUS\tgene\t3467\t6217\t0.78\t-\t.\tg4\r\n", "scaffold7_cov100\t6144\t6146\tscaffold7_cov100\tAUGUSTUS\tgene\t3467\t6217\t0.78\t-\t.\tg4\r\n", "\r\n", "==> Meth9_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-Meth.bed-paGenes <==\r\n", "scaffold7_cov100\t5986\t5988\tscaffold7_cov100\tAUGUSTUS\tgene\t3467\t6217\t0.78\t-\t.\tg4\r\n", "scaffold7_cov100\t6144\t6146\tscaffold7_cov100\tAUGUSTUS\tgene\t3467\t6217\t0.78\t-\t.\tg4\r\n", "scaffold7_cov100\t6188\t6190\tscaffold7_cov100\tAUGUSTUS\tgene\t3467\t6217\t0.78\t-\t.\tg4\r\n", "scaffold7_cov100\t6198\t6200\tscaffold7_cov100\tAUGUSTUS\tgene\t3467\t6217\t0.78\t-\t.\tg4\r\n", "scaffold7_cov100\t7438\t7440\tscaffold7_cov100\tAUGUSTUS\tgene\t7069\t9073\t1\t-\t.\tg5\r\n", "scaffold7_cov100\t7696\t7698\tscaffold7_cov100\tAUGUSTUS\tgene\t7069\t9073\t1\t-\t.\tg5\r\n", "scaffold7_cov100\t7796\t7798\tscaffold7_cov100\tAUGUSTUS\tgene\t7069\t9073\t1\t-\t.\tg5\r\n", "scaffold7_cov100\t7891\t7893\tscaffold7_cov100\tAUGUSTUS\tgene\t7069\t9073\t1\t-\t.\tg5\r\n", "scaffold7_cov100\t9877\t9879\tscaffold7_cov100\tAUGUSTUS\tgene\t9590\t11670\t0.8\t-\t.\tg6\r\n", "scaffold7_cov100\t10216\t10218\tscaffold7_cov100\tAUGUSTUS\tgene\t9590\t11670\t0.8\t-\t.\tg6\r\n", "\r\n", "==> Meth9_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-sparseMeth.bed-paGenes <==\r\n", "scaffold6_cov64\t3435\t3437\tscaffold6_cov64\tAUGUSTUS\tgene\t1\t5652\t0.46\t-\t.\tg1\r\n", "scaffold7_cov100\t10755\t10757\tscaffold7_cov100\tAUGUSTUS\tgene\t9590\t11670\t0.8\t-\t.\tg6\r\n", "scaffold7_cov100\t14042\t14044\tscaffold7_cov100\tAUGUSTUS\tgene\t13339\t15463\t0.92\t-\t.\tg7\r\n", "scaffold7_cov100\t17952\t17954\tscaffold7_cov100\tAUGUSTUS\tgene\t15738\t18320\t0.96\t+\t.\tg8\r\n", "scaffold7_cov100\t20473\t20475\tscaffold7_cov100\tAUGUSTUS\tgene\t20078\t24295\t0.39\t+\t.\tg11\r\n", "scaffold7_cov100\t46359\t46361\tscaffold7_cov100\tAUGUSTUS\tgene\t41188\t47537\t0.97\t+\t.\tg14\r\n", "scaffold7_cov100\t69268\t69270\tscaffold7_cov100\tAUGUSTUS\tgene\t68185\t73140\t1\t-\t.\tg18\r\n", "scaffold7_cov100\t69313\t69315\tscaffold7_cov100\tAUGUSTUS\tgene\t68185\t73140\t1\t-\t.\tg18\r\n", "scaffold7_cov100\t75788\t75790\tscaffold7_cov100\tAUGUSTUS\tgene\t75096\t77075\t0.91\t-\t.\tg19\r\n", "scaffold7_cov100\t75920\t75922\tscaffold7_cov100\tAUGUSTUS\tgene\t75096\t77075\t0.91\t-\t.\tg19\r\n", "\r\n", "==> Meth9_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-unMeth.bed-paGenes <==\r\n", "scaffold6_cov64\t298\t300\tscaffold6_cov64\tAUGUSTUS\tgene\t1\t5652\t0.46\t-\t.\tg1\r\n", "scaffold6_cov64\t489\t491\tscaffold6_cov64\tAUGUSTUS\tgene\t1\t5652\t0.46\t-\t.\tg1\r\n", "scaffold6_cov64\t2179\t2181\tscaffold6_cov64\tAUGUSTUS\tgene\t1\t5652\t0.46\t-\t.\tg1\r\n", "scaffold6_cov64\t3412\t3414\tscaffold6_cov64\tAUGUSTUS\tgene\t1\t5652\t0.46\t-\t.\tg1\r\n", "scaffold6_cov64\t3420\t3422\tscaffold6_cov64\tAUGUSTUS\tgene\t1\t5652\t0.46\t-\t.\tg1\r\n", "scaffold6_cov64\t3439\t3441\tscaffold6_cov64\tAUGUSTUS\tgene\t1\t5652\t0.46\t-\t.\tg1\r\n", "scaffold6_cov64\t3444\t3446\tscaffold6_cov64\tAUGUSTUS\tgene\t1\t5652\t0.46\t-\t.\tg1\r\n", "scaffold6_cov64\t3507\t3509\tscaffold6_cov64\tAUGUSTUS\tgene\t1\t5652\t0.46\t-\t.\tg1\r\n", "scaffold6_cov64\t3569\t3571\tscaffold6_cov64\tAUGUSTUS\tgene\t1\t5652\t0.46\t-\t.\tg1\r\n", "scaffold6_cov64\t5101\t5103\tscaffold6_cov64\tAUGUSTUS\tgene\t1\t5652\t0.46\t-\t.\tg1\r\n", "\r\n", "==> Meth9_R1_001_val_1_bismark_bt2_pe._10x.bedgraph.bed-paGenes <==\r\n", "scaffold6_cov64\t298\t300\tscaffold6_cov64\tAUGUSTUS\tgene\t1\t5652\t0.46\t-\t.\tg1\r\n", "scaffold6_cov64\t489\t491\tscaffold6_cov64\tAUGUSTUS\tgene\t1\t5652\t0.46\t-\t.\tg1\r\n", "scaffold6_cov64\t2179\t2181\tscaffold6_cov64\tAUGUSTUS\tgene\t1\t5652\t0.46\t-\t.\tg1\r\n", "scaffold6_cov64\t3412\t3414\tscaffold6_cov64\tAUGUSTUS\tgene\t1\t5652\t0.46\t-\t.\tg1\r\n", "scaffold6_cov64\t3420\t3422\tscaffold6_cov64\tAUGUSTUS\tgene\t1\t5652\t0.46\t-\t.\tg1\r\n", "scaffold6_cov64\t3435\t3437\tscaffold6_cov64\tAUGUSTUS\tgene\t1\t5652\t0.46\t-\t.\tg1\r\n", "scaffold6_cov64\t3439\t3441\tscaffold6_cov64\tAUGUSTUS\tgene\t1\t5652\t0.46\t-\t.\tg1\r\n", "scaffold6_cov64\t3444\t3446\tscaffold6_cov64\tAUGUSTUS\tgene\t1\t5652\t0.46\t-\t.\tg1\r\n", "scaffold6_cov64\t3507\t3509\tscaffold6_cov64\tAUGUSTUS\tgene\t1\t5652\t0.46\t-\t.\tg1\r\n", "scaffold6_cov64\t3569\t3571\tscaffold6_cov64\tAUGUSTUS\tgene\t1\t5652\t0.46\t-\t.\tg1\r\n" ] } ], "source": [ "#Check output\n", "!head *paGenes" ] }, { "cell_type": "code", "execution_count": 104, "metadata": { "scrolled": true }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ " 25899 Meth1_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-Meth.bed-paGenes\n", " 34626 Meth1_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-sparseMeth.bed-paGenes\n", " 1118909 Meth1_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-unMeth.bed-paGenes\n", " 1179434 Meth1_R1_001_val_1_bismark_bt2_pe._10x.bedgraph.bed-paGenes\n", " 47716 Meth2_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-Meth.bed-paGenes\n", " 49984 Meth2_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-sparseMeth.bed-paGenes\n", " 1723334 Meth2_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-unMeth.bed-paGenes\n", " 1821034 Meth2_R1_001_val_1_bismark_bt2_pe._10x.bedgraph.bed-paGenes\n", " 35357 Meth3_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-Meth.bed-paGenes\n", " 44108 Meth3_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-sparseMeth.bed-paGenes\n", " 1346622 Meth3_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-unMeth.bed-paGenes\n", " 1426087 Meth3_R1_001_val_1_bismark_bt2_pe._10x.bedgraph.bed-paGenes\n", " 4988 Meth4_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-Meth.bed-paGenes\n", " 26205 Meth4_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-sparseMeth.bed-paGenes\n", " 471620 Meth4_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-unMeth.bed-paGenes\n", " 502813 Meth4_R1_001_val_1_bismark_bt2_pe._10x.bedgraph.bed-paGenes\n", " 5815 Meth5_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-Meth.bed-paGenes\n", " 10664 Meth5_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-sparseMeth.bed-paGenes\n", " 399537 Meth5_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-unMeth.bed-paGenes\n", " 416016 Meth5_R1_001_val_1_bismark_bt2_pe._10x.bedgraph.bed-paGenes\n", " 4293 Meth6_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-Meth.bed-paGenes\n", " 14614 Meth6_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-sparseMeth.bed-paGenes\n", " 409911 Meth6_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-unMeth.bed-paGenes\n", " 428818 Meth6_R1_001_val_1_bismark_bt2_pe._10x.bedgraph.bed-paGenes\n", " 87468 Meth7_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-Meth.bed-paGenes\n", " 31803 Meth7_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-sparseMeth.bed-paGenes\n", " 206218 Meth7_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-unMeth.bed-paGenes\n", " 325489 Meth7_R1_001_val_1_bismark_bt2_pe._10x.bedgraph.bed-paGenes\n", " 60278 Meth8_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-Meth.bed-paGenes\n", " 11894 Meth8_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-sparseMeth.bed-paGenes\n", " 16503 Meth8_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-unMeth.bed-paGenes\n", " 88675 Meth8_R1_001_val_1_bismark_bt2_pe._10x.bedgraph.bed-paGenes\n", " 92131 Meth9_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-Meth.bed-paGenes\n", " 34146 Meth9_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-sparseMeth.bed-paGenes\n", " 188462 Meth9_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-unMeth.bed-paGenes\n", " 314739 Meth9_R1_001_val_1_bismark_bt2_pe._10x.bedgraph.bed-paGenes\n", " 13006210 total\n" ] } ], "source": [ "#Count number of overlaps\n", "!wc -l *paGenes" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "#### 4c. Coding Sequences (CDS)" ] }, { "cell_type": "code", "execution_count": 105, "metadata": { "collapsed": true, "scrolled": true }, "outputs": [], "source": [ "%%bash\n", "\n", "for f in *bed\n", "do\n", " /usr/local/bin/intersectBed \\\n", " -wb \\\n", " -a ${f} \\\n", " -b ../../../genome-feature-files/Pact.GFFannotation.CDS.gff \\\n", " > ${f}-paCDS\n", "done" ] }, { "cell_type": "code", "execution_count": 106, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "==> Meth1_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-Meth.bed-paCDS <==\r\n", "scaffold7_cov100\t6144\t6146\tscaffold7_cov100\tAUGUSTUS\tCDS\t6091\t6217\t0.48\t-\t0\ttranscript_id \"g4.t1\"; gene_id \"g4\";\r\n", "scaffold7_cov100\t6144\t6146\tscaffold7_cov100\tAUGUSTUS\tCDS\t6091\t6211\t0.52\t-\t0\ttranscript_id \"g4.t2\"; gene_id \"g4\";\r\n", "scaffold7_cov100\t6188\t6190\tscaffold7_cov100\tAUGUSTUS\tCDS\t6091\t6217\t0.48\t-\t0\ttranscript_id \"g4.t1\"; gene_id \"g4\";\r\n", "scaffold7_cov100\t6188\t6190\tscaffold7_cov100\tAUGUSTUS\tCDS\t6091\t6211\t0.52\t-\t0\ttranscript_id \"g4.t2\"; gene_id \"g4\";\r\n", "scaffold7_cov100\t7892\t7893\tscaffold7_cov100\tAUGUSTUS\tCDS\t7893\t7980\t1\t-\t0\ttranscript_id \"g5.t1\"; gene_id \"g5\";\r\n", "scaffold7_cov100\t7892\t7893\tscaffold7_cov100\tAUGUSTUS\tCDS\t7893\t7980\t1\t-\t0\ttranscript_id \"g5.t2\"; gene_id \"g5\";\r\n", "scaffold7_cov100\t8323\t8325\tscaffold7_cov100\tAUGUSTUS\tCDS\t8286\t8363\t1\t-\t0\ttranscript_id \"g5.t1\"; gene_id \"g5\";\r\n", "scaffold7_cov100\t8323\t8325\tscaffold7_cov100\tAUGUSTUS\tCDS\t8286\t8363\t1\t-\t0\ttranscript_id \"g5.t2\"; gene_id \"g5\";\r\n", "scaffold7_cov100\t9877\t9879\tscaffold7_cov100\tAUGUSTUS\tCDS\t9856\t9926\t1\t-\t2\ttranscript_id \"g6.t1\"; gene_id \"g6\";\r\n", "scaffold7_cov100\t10216\t10218\tscaffold7_cov100\tAUGUSTUS\tCDS\t10200\t10281\t1\t-\t0\ttranscript_id \"g6.t1\"; gene_id \"g6\";\r\n", "\r\n", "==> Meth1_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-sparseMeth.bed-paCDS <==\r\n", "scaffold7_cov100\t1293\t1295\tscaffold7_cov100\tAUGUSTUS\tCDS\t1\t2566\t0.96\t+\t1\ttranscript_id \"g3.t1\"; gene_id \"g3\";\r\n", "scaffold7_cov100\t2289\t2291\tscaffold7_cov100\tAUGUSTUS\tCDS\t1\t2566\t0.96\t+\t1\ttranscript_id \"g3.t1\"; gene_id \"g3\";\r\n", "scaffold7_cov100\t9715\t9717\tscaffold7_cov100\tAUGUSTUS\tCDS\t9590\t9724\t1\t-\t0\ttranscript_id \"g6.t1\"; gene_id \"g6\";\r\n", "scaffold7_cov100\t17098\t17100\tscaffold7_cov100\tAUGUSTUS\tCDS\t15738\t18320\t0.53\t+\t0\ttranscript_id \"g8.t1\"; gene_id \"g8\";\r\n", "scaffold7_cov100\t17098\t17100\tscaffold7_cov100\tAUGUSTUS\tCDS\t15789\t18320\t0.43\t+\t0\ttranscript_id \"g8.t2\"; gene_id \"g8\";\r\n", "scaffold7_cov100\t17952\t17954\tscaffold7_cov100\tAUGUSTUS\tCDS\t15738\t18320\t0.53\t+\t0\ttranscript_id \"g8.t1\"; gene_id \"g8\";\r\n", "scaffold7_cov100\t17952\t17954\tscaffold7_cov100\tAUGUSTUS\tCDS\t15789\t18320\t0.43\t+\t0\ttranscript_id \"g8.t2\"; gene_id \"g8\";\r\n", "scaffold7_cov100\t20473\t20475\tscaffold7_cov100\tAUGUSTUS\tCDS\t20394\t20696\t0.71\t+\t0\ttranscript_id \"g11.t1\"; gene_id \"g11\";\r\n", "scaffold7_cov100\t29019\t29021\tscaffold7_cov100\tAUGUSTUS\tCDS\t28517\t29779\t0.69\t-\t0\ttranscript_id \"g12.t1\"; gene_id \"g12\";\r\n", "scaffold7_cov100\t45742\t45744\tscaffold7_cov100\tAUGUSTUS\tCDS\t45637\t46757\t1\t+\t2\ttranscript_id \"g14.t1\"; gene_id \"g14\";\r\n", "\r\n", "==> Meth1_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-unMeth.bed-paCDS <==\r\n", "scaffold6_cov64\t826\t828\tscaffold6_cov64\tAUGUSTUS\tCDS\t495\t842\t0.84\t-\t2\ttranscript_id \"g1.t1\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t826\t828\tscaffold6_cov64\tAUGUSTUS\tCDS\t495\t842\t0.84\t-\t2\ttranscript_id \"g1.t2\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t2179\t2181\tscaffold6_cov64\tAUGUSTUS\tCDS\t1922\t2269\t1\t-\t2\ttranscript_id \"g1.t1\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t2179\t2181\tscaffold6_cov64\tAUGUSTUS\tCDS\t1922\t2269\t1\t-\t2\ttranscript_id \"g1.t2\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t4793\t4795\tscaffold6_cov64\tAUGUSTUS\tCDS\t4754\t4851\t0.4\t-\t1\ttranscript_id \"g1.t2\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t5582\t5583\tscaffold6_cov64\tAUGUSTUS\tCDS\t5583\t5652\t0.26\t-\t0\ttranscript_id \"g1.t1\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t5583\t5585\tscaffold6_cov64\tAUGUSTUS\tCDS\t5583\t5652\t0.26\t-\t0\ttranscript_id \"g1.t1\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t5592\t5594\tscaffold6_cov64\tAUGUSTUS\tCDS\t5583\t5652\t0.26\t-\t0\ttranscript_id \"g1.t1\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t5593\t5594\tscaffold6_cov64\tAUGUSTUS\tCDS\t5594\t5652\t0.54\t-\t0\ttranscript_id \"g1.t2\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t5594\t5596\tscaffold6_cov64\tAUGUSTUS\tCDS\t5583\t5652\t0.26\t-\t0\ttranscript_id \"g1.t1\"; gene_id \"g1\";\r\n", "\r\n", "==> Meth1_R1_001_val_1_bismark_bt2_pe._10x.bedgraph.bed-paCDS <==\r\n", "scaffold6_cov64\t826\t828\tscaffold6_cov64\tAUGUSTUS\tCDS\t495\t842\t0.84\t-\t2\ttranscript_id \"g1.t1\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t826\t828\tscaffold6_cov64\tAUGUSTUS\tCDS\t495\t842\t0.84\t-\t2\ttranscript_id \"g1.t2\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t2179\t2181\tscaffold6_cov64\tAUGUSTUS\tCDS\t1922\t2269\t1\t-\t2\ttranscript_id \"g1.t1\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t2179\t2181\tscaffold6_cov64\tAUGUSTUS\tCDS\t1922\t2269\t1\t-\t2\ttranscript_id \"g1.t2\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t4793\t4795\tscaffold6_cov64\tAUGUSTUS\tCDS\t4754\t4851\t0.4\t-\t1\ttranscript_id \"g1.t2\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t5582\t5583\tscaffold6_cov64\tAUGUSTUS\tCDS\t5583\t5652\t0.26\t-\t0\ttranscript_id \"g1.t1\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t5583\t5585\tscaffold6_cov64\tAUGUSTUS\tCDS\t5583\t5652\t0.26\t-\t0\ttranscript_id \"g1.t1\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t5592\t5594\tscaffold6_cov64\tAUGUSTUS\tCDS\t5583\t5652\t0.26\t-\t0\ttranscript_id \"g1.t1\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t5593\t5594\tscaffold6_cov64\tAUGUSTUS\tCDS\t5594\t5652\t0.54\t-\t0\ttranscript_id \"g1.t2\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t5594\t5596\tscaffold6_cov64\tAUGUSTUS\tCDS\t5583\t5652\t0.26\t-\t0\ttranscript_id \"g1.t1\"; gene_id \"g1\";\r\n", "\r\n", "==> Meth2_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-Meth.bed-paCDS <==\r\n", "scaffold7_cov100\t5500\t5502\tscaffold7_cov100\tAUGUSTUS\tCDS\t5466\t5540\t1\t-\t2\ttranscript_id \"g4.t1\"; gene_id \"g4\";\r\n", "scaffold7_cov100\t5500\t5502\tscaffold7_cov100\tAUGUSTUS\tCDS\t5466\t5540\t1\t-\t2\ttranscript_id \"g4.t2\"; gene_id \"g4\";\r\n", "scaffold7_cov100\t6144\t6146\tscaffold7_cov100\tAUGUSTUS\tCDS\t6091\t6217\t0.48\t-\t0\ttranscript_id \"g4.t1\"; gene_id \"g4\";\r\n", "scaffold7_cov100\t6144\t6146\tscaffold7_cov100\tAUGUSTUS\tCDS\t6091\t6211\t0.52\t-\t0\ttranscript_id \"g4.t2\"; gene_id \"g4\";\r\n", "scaffold7_cov100\t6188\t6190\tscaffold7_cov100\tAUGUSTUS\tCDS\t6091\t6217\t0.48\t-\t0\ttranscript_id \"g4.t1\"; gene_id \"g4\";\r\n", "scaffold7_cov100\t6188\t6190\tscaffold7_cov100\tAUGUSTUS\tCDS\t6091\t6211\t0.52\t-\t0\ttranscript_id \"g4.t2\"; gene_id \"g4\";\r\n", "scaffold7_cov100\t6198\t6200\tscaffold7_cov100\tAUGUSTUS\tCDS\t6091\t6217\t0.48\t-\t0\ttranscript_id \"g4.t1\"; gene_id \"g4\";\r\n", "scaffold7_cov100\t6198\t6200\tscaffold7_cov100\tAUGUSTUS\tCDS\t6091\t6211\t0.52\t-\t0\ttranscript_id \"g4.t2\"; gene_id \"g4\";\r\n", "scaffold7_cov100\t7696\t7698\tscaffold7_cov100\tAUGUSTUS\tCDS\t7650\t7715\t1\t-\t2\ttranscript_id \"g5.t1\"; gene_id \"g5\";\r\n", "scaffold7_cov100\t7696\t7698\tscaffold7_cov100\tAUGUSTUS\tCDS\t7650\t7715\t1\t-\t2\ttranscript_id \"g5.t2\"; gene_id \"g5\";\r\n", "\r\n", "==> Meth2_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-sparseMeth.bed-paCDS <==\r\n", "scaffold7_cov100\t10755\t10757\tscaffold7_cov100\tAUGUSTUS\tCDS\t10595\t10789\t0.95\t-\t0\ttranscript_id \"g6.t1\"; gene_id \"g6\";\r\n", "scaffold7_cov100\t16874\t16876\tscaffold7_cov100\tAUGUSTUS\tCDS\t15738\t18320\t0.53\t+\t0\ttranscript_id \"g8.t1\"; gene_id \"g8\";\r\n", "scaffold7_cov100\t16874\t16876\tscaffold7_cov100\tAUGUSTUS\tCDS\t15789\t18320\t0.43\t+\t0\ttranscript_id \"g8.t2\"; gene_id \"g8\";\r\n", "scaffold7_cov100\t17074\t17076\tscaffold7_cov100\tAUGUSTUS\tCDS\t15738\t18320\t0.53\t+\t0\ttranscript_id \"g8.t1\"; gene_id \"g8\";\r\n", "scaffold7_cov100\t17074\t17076\tscaffold7_cov100\tAUGUSTUS\tCDS\t15789\t18320\t0.43\t+\t0\ttranscript_id \"g8.t2\"; gene_id \"g8\";\r\n", "scaffold7_cov100\t17098\t17100\tscaffold7_cov100\tAUGUSTUS\tCDS\t15738\t18320\t0.53\t+\t0\ttranscript_id \"g8.t1\"; gene_id \"g8\";\r\n", "scaffold7_cov100\t17098\t17100\tscaffold7_cov100\tAUGUSTUS\tCDS\t15789\t18320\t0.43\t+\t0\ttranscript_id \"g8.t2\"; gene_id \"g8\";\r\n", "scaffold7_cov100\t17212\t17214\tscaffold7_cov100\tAUGUSTUS\tCDS\t15738\t18320\t0.53\t+\t0\ttranscript_id \"g8.t1\"; gene_id \"g8\";\r\n", "scaffold7_cov100\t17212\t17214\tscaffold7_cov100\tAUGUSTUS\tCDS\t15789\t18320\t0.43\t+\t0\ttranscript_id \"g8.t2\"; gene_id \"g8\";\r\n", "scaffold7_cov100\t19339\t19341\tscaffold7_cov100\tAUGUSTUS\tCDS\t19312\t19534\t0.29\t+\t0\ttranscript_id \"g10.t1\"; gene_id \"g10\";\r\n", "\r\n", "==> Meth2_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-unMeth.bed-paCDS <==\r\n", "scaffold6_cov64\t826\t828\tscaffold6_cov64\tAUGUSTUS\tCDS\t495\t842\t0.84\t-\t2\ttranscript_id \"g1.t1\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t826\t828\tscaffold6_cov64\tAUGUSTUS\tCDS\t495\t842\t0.84\t-\t2\ttranscript_id \"g1.t2\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t2097\t2099\tscaffold6_cov64\tAUGUSTUS\tCDS\t1922\t2269\t1\t-\t2\ttranscript_id \"g1.t1\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t2097\t2099\tscaffold6_cov64\tAUGUSTUS\tCDS\t1922\t2269\t1\t-\t2\ttranscript_id \"g1.t2\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t2179\t2181\tscaffold6_cov64\tAUGUSTUS\tCDS\t1922\t2269\t1\t-\t2\ttranscript_id \"g1.t1\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t2179\t2181\tscaffold6_cov64\tAUGUSTUS\tCDS\t1922\t2269\t1\t-\t2\ttranscript_id \"g1.t2\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t2253\t2255\tscaffold6_cov64\tAUGUSTUS\tCDS\t1922\t2269\t1\t-\t2\ttranscript_id \"g1.t1\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t2253\t2255\tscaffold6_cov64\tAUGUSTUS\tCDS\t1922\t2269\t1\t-\t2\ttranscript_id \"g1.t2\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t4793\t4795\tscaffold6_cov64\tAUGUSTUS\tCDS\t4754\t4851\t0.4\t-\t1\ttranscript_id \"g1.t2\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t5582\t5583\tscaffold6_cov64\tAUGUSTUS\tCDS\t5583\t5652\t0.26\t-\t0\ttranscript_id \"g1.t1\"; gene_id \"g1\";\r\n", "\r\n", "==> Meth2_R1_001_val_1_bismark_bt2_pe._10x.bedgraph.bed-paCDS <==\r\n", "scaffold6_cov64\t826\t828\tscaffold6_cov64\tAUGUSTUS\tCDS\t495\t842\t0.84\t-\t2\ttranscript_id \"g1.t1\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t826\t828\tscaffold6_cov64\tAUGUSTUS\tCDS\t495\t842\t0.84\t-\t2\ttranscript_id \"g1.t2\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t2097\t2099\tscaffold6_cov64\tAUGUSTUS\tCDS\t1922\t2269\t1\t-\t2\ttranscript_id \"g1.t1\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t2097\t2099\tscaffold6_cov64\tAUGUSTUS\tCDS\t1922\t2269\t1\t-\t2\ttranscript_id \"g1.t2\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t2179\t2181\tscaffold6_cov64\tAUGUSTUS\tCDS\t1922\t2269\t1\t-\t2\ttranscript_id \"g1.t1\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t2179\t2181\tscaffold6_cov64\tAUGUSTUS\tCDS\t1922\t2269\t1\t-\t2\ttranscript_id \"g1.t2\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t2253\t2255\tscaffold6_cov64\tAUGUSTUS\tCDS\t1922\t2269\t1\t-\t2\ttranscript_id \"g1.t1\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t2253\t2255\tscaffold6_cov64\tAUGUSTUS\tCDS\t1922\t2269\t1\t-\t2\ttranscript_id \"g1.t2\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t4793\t4795\tscaffold6_cov64\tAUGUSTUS\tCDS\t4754\t4851\t0.4\t-\t1\ttranscript_id \"g1.t2\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t5582\t5583\tscaffold6_cov64\tAUGUSTUS\tCDS\t5583\t5652\t0.26\t-\t0\ttranscript_id \"g1.t1\"; gene_id \"g1\";\r\n", "\r\n", "==> Meth3_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-Meth.bed-paCDS <==\r\n", "scaffold7_cov100\t7696\t7698\tscaffold7_cov100\tAUGUSTUS\tCDS\t7650\t7715\t1\t-\t2\ttranscript_id \"g5.t1\"; gene_id \"g5\";\r\n", "scaffold7_cov100\t7696\t7698\tscaffold7_cov100\tAUGUSTUS\tCDS\t7650\t7715\t1\t-\t2\ttranscript_id \"g5.t2\"; gene_id \"g5\";\r\n", "scaffold7_cov100\t9877\t9879\tscaffold7_cov100\tAUGUSTUS\tCDS\t9856\t9926\t1\t-\t2\ttranscript_id \"g6.t1\"; gene_id \"g6\";\r\n", "scaffold7_cov100\t10273\t10275\tscaffold7_cov100\tAUGUSTUS\tCDS\t10200\t10281\t1\t-\t0\ttranscript_id \"g6.t1\"; gene_id \"g6\";\r\n", "scaffold7_cov100\t11043\t11045\tscaffold7_cov100\tAUGUSTUS\tCDS\t11015\t11101\t1\t-\t0\ttranscript_id \"g6.t1\"; gene_id \"g6\";\r\n", "scaffold7_cov100\t17527\t17529\tscaffold7_cov100\tAUGUSTUS\tCDS\t15738\t18320\t0.53\t+\t0\ttranscript_id \"g8.t1\"; gene_id \"g8\";\r\n", "scaffold7_cov100\t17527\t17529\tscaffold7_cov100\tAUGUSTUS\tCDS\t15789\t18320\t0.43\t+\t0\ttranscript_id \"g8.t2\"; gene_id \"g8\";\r\n", "scaffold7_cov100\t17552\t17554\tscaffold7_cov100\tAUGUSTUS\tCDS\t15738\t18320\t0.53\t+\t0\ttranscript_id \"g8.t1\"; gene_id \"g8\";\r\n", "scaffold7_cov100\t17552\t17554\tscaffold7_cov100\tAUGUSTUS\tCDS\t15789\t18320\t0.43\t+\t0\ttranscript_id \"g8.t2\"; gene_id \"g8\";\r\n", "scaffold7_cov100\t17633\t17635\tscaffold7_cov100\tAUGUSTUS\tCDS\t15738\t18320\t0.53\t+\t0\ttranscript_id \"g8.t1\"; gene_id \"g8\";\r\n", "\r\n", "==> Meth3_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-sparseMeth.bed-paCDS <==\r\n", "scaffold7_cov100\t4630\t4632\tscaffold7_cov100\tAUGUSTUS\tCDS\t4608\t4780\t1\t-\t2\ttranscript_id \"g4.t1\"; gene_id \"g4\";\r\n", "scaffold7_cov100\t4630\t4632\tscaffold7_cov100\tAUGUSTUS\tCDS\t4608\t4780\t1\t-\t2\ttranscript_id \"g4.t2\"; gene_id \"g4\";\r\n", "scaffold7_cov100\t4678\t4680\tscaffold7_cov100\tAUGUSTUS\tCDS\t4608\t4780\t1\t-\t2\ttranscript_id \"g4.t1\"; gene_id \"g4\";\r\n", "scaffold7_cov100\t4678\t4680\tscaffold7_cov100\tAUGUSTUS\tCDS\t4608\t4780\t1\t-\t2\ttranscript_id \"g4.t2\"; gene_id \"g4\";\r\n", "scaffold7_cov100\t9715\t9717\tscaffold7_cov100\tAUGUSTUS\tCDS\t9590\t9724\t1\t-\t0\ttranscript_id \"g6.t1\"; gene_id \"g6\";\r\n", "scaffold7_cov100\t17212\t17214\tscaffold7_cov100\tAUGUSTUS\tCDS\t15738\t18320\t0.53\t+\t0\ttranscript_id \"g8.t1\"; gene_id \"g8\";\r\n", "scaffold7_cov100\t17212\t17214\tscaffold7_cov100\tAUGUSTUS\tCDS\t15789\t18320\t0.43\t+\t0\ttranscript_id \"g8.t2\"; gene_id \"g8\";\r\n", "scaffold7_cov100\t17952\t17954\tscaffold7_cov100\tAUGUSTUS\tCDS\t15738\t18320\t0.53\t+\t0\ttranscript_id \"g8.t1\"; gene_id \"g8\";\r\n", "scaffold7_cov100\t17952\t17954\tscaffold7_cov100\tAUGUSTUS\tCDS\t15789\t18320\t0.43\t+\t0\ttranscript_id \"g8.t2\"; gene_id \"g8\";\r\n", "scaffold7_cov100\t20473\t20475\tscaffold7_cov100\tAUGUSTUS\tCDS\t20394\t20696\t0.71\t+\t0\ttranscript_id \"g11.t1\"; gene_id \"g11\";\r\n", "\r\n", "==> Meth3_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-unMeth.bed-paCDS <==\r\n", "scaffold6_cov64\t826\t828\tscaffold6_cov64\tAUGUSTUS\tCDS\t495\t842\t0.84\t-\t2\ttranscript_id \"g1.t1\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t826\t828\tscaffold6_cov64\tAUGUSTUS\tCDS\t495\t842\t0.84\t-\t2\ttranscript_id \"g1.t2\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t2179\t2181\tscaffold6_cov64\tAUGUSTUS\tCDS\t1922\t2269\t1\t-\t2\ttranscript_id \"g1.t1\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t2179\t2181\tscaffold6_cov64\tAUGUSTUS\tCDS\t1922\t2269\t1\t-\t2\ttranscript_id \"g1.t2\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t4793\t4795\tscaffold6_cov64\tAUGUSTUS\tCDS\t4754\t4851\t0.4\t-\t1\ttranscript_id \"g1.t2\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t5582\t5583\tscaffold6_cov64\tAUGUSTUS\tCDS\t5583\t5652\t0.26\t-\t0\ttranscript_id \"g1.t1\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t5583\t5585\tscaffold6_cov64\tAUGUSTUS\tCDS\t5583\t5652\t0.26\t-\t0\ttranscript_id \"g1.t1\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t5592\t5594\tscaffold6_cov64\tAUGUSTUS\tCDS\t5583\t5652\t0.26\t-\t0\ttranscript_id \"g1.t1\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t5593\t5594\tscaffold6_cov64\tAUGUSTUS\tCDS\t5594\t5652\t0.54\t-\t0\ttranscript_id \"g1.t2\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t5594\t5596\tscaffold6_cov64\tAUGUSTUS\tCDS\t5583\t5652\t0.26\t-\t0\ttranscript_id \"g1.t1\"; gene_id \"g1\";\r\n", "\r\n", "==> Meth3_R1_001_val_1_bismark_bt2_pe._10x.bedgraph.bed-paCDS <==\r\n", "scaffold6_cov64\t826\t828\tscaffold6_cov64\tAUGUSTUS\tCDS\t495\t842\t0.84\t-\t2\ttranscript_id \"g1.t1\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t826\t828\tscaffold6_cov64\tAUGUSTUS\tCDS\t495\t842\t0.84\t-\t2\ttranscript_id \"g1.t2\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t2179\t2181\tscaffold6_cov64\tAUGUSTUS\tCDS\t1922\t2269\t1\t-\t2\ttranscript_id \"g1.t1\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t2179\t2181\tscaffold6_cov64\tAUGUSTUS\tCDS\t1922\t2269\t1\t-\t2\ttranscript_id \"g1.t2\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t4793\t4795\tscaffold6_cov64\tAUGUSTUS\tCDS\t4754\t4851\t0.4\t-\t1\ttranscript_id \"g1.t2\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t5582\t5583\tscaffold6_cov64\tAUGUSTUS\tCDS\t5583\t5652\t0.26\t-\t0\ttranscript_id \"g1.t1\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t5583\t5585\tscaffold6_cov64\tAUGUSTUS\tCDS\t5583\t5652\t0.26\t-\t0\ttranscript_id \"g1.t1\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t5592\t5594\tscaffold6_cov64\tAUGUSTUS\tCDS\t5583\t5652\t0.26\t-\t0\ttranscript_id \"g1.t1\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t5593\t5594\tscaffold6_cov64\tAUGUSTUS\tCDS\t5594\t5652\t0.54\t-\t0\ttranscript_id \"g1.t2\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t5594\t5596\tscaffold6_cov64\tAUGUSTUS\tCDS\t5583\t5652\t0.26\t-\t0\ttranscript_id \"g1.t1\"; gene_id \"g1\";\r\n", "\r\n", "==> Meth4_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-Meth.bed-paCDS <==\r\n", "scaffold7_cov100\t96791\t96793\tscaffold7_cov100\tAUGUSTUS\tCDS\t96783\t96869\t0.96\t-\t0\ttranscript_id \"g24.t1\"; gene_id \"g24\";\r\n", "scaffold7_cov100\t96791\t96793\tscaffold7_cov100\tAUGUSTUS\tCDS\t96783\t96869\t0.96\t-\t0\ttranscript_id \"g24.t2\"; gene_id \"g24\";\r\n", "scaffold7_cov100\t338971\t338973\tscaffold7_cov100\tAUGUSTUS\tCDS\t338812\t339072\t1\t+\t0\ttranscript_id \"g74.t1\"; gene_id \"g74\";\r\n", "scaffold7_cov100\t360165\t360167\tscaffold7_cov100\tAUGUSTUS\tCDS\t359591\t360506\t0.93\t-\t1\ttranscript_id \"g79.t1\"; gene_id \"g79\";\r\n", "scaffold7_cov100\t360165\t360167\tscaffold7_cov100\tAUGUSTUS\tCDS\t359591\t360506\t0.93\t-\t1\ttranscript_id \"g79.t2\"; gene_id \"g79\";\r\n", "scaffold7_cov100\t403347\t403349\tscaffold7_cov100\tAUGUSTUS\tCDS\t403291\t403478\t1\t+\t0\ttranscript_id \"g87.t1\"; gene_id \"g87\";\r\n", "scaffold7_cov100\t403347\t403349\tscaffold7_cov100\tAUGUSTUS\tCDS\t403291\t403478\t1\t+\t0\ttranscript_id \"g87.t2\"; gene_id \"g87\";\r\n", "scaffold7_cov100\t403727\t403729\tscaffold7_cov100\tAUGUSTUS\tCDS\t403652\t403885\t1\t+\t1\ttranscript_id \"g87.t1\"; gene_id \"g87\";\r\n", "scaffold7_cov100\t403727\t403729\tscaffold7_cov100\tAUGUSTUS\tCDS\t403652\t403885\t1\t+\t1\ttranscript_id \"g87.t2\"; gene_id \"g87\";\r\n", "scaffold7_cov100\t440492\t440494\tscaffold7_cov100\tAUGUSTUS\tCDS\t440241\t440754\t0.92\t-\t0\ttranscript_id \"g94.t1\"; gene_id \"g94\";\r\n", "\r\n", "==> Meth4_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-sparseMeth.bed-paCDS <==\r\n", "scaffold7_cov100\t46343\t46345\tscaffold7_cov100\tAUGUSTUS\tCDS\t45637\t46757\t1\t+\t2\ttranscript_id \"g14.t1\"; gene_id \"g14\";\r\n", "scaffold7_cov100\t46397\t46399\tscaffold7_cov100\tAUGUSTUS\tCDS\t45637\t46757\t1\t+\t2\ttranscript_id \"g14.t1\"; gene_id \"g14\";\r\n", "scaffold7_cov100\t55479\t55481\tscaffold7_cov100\tAUGUSTUS\tCDS\t55439\t55521\t1\t+\t2\ttranscript_id \"g16.t1\"; gene_id \"g16\";\r\n", "scaffold7_cov100\t61080\t61082\tscaffold7_cov100\tAUGUSTUS\tCDS\t61010\t61128\t1\t+\t0\ttranscript_id \"g16.t1\"; gene_id \"g16\";\r\n", "scaffold7_cov100\t91942\t91943\tscaffold7_cov100\tAUGUSTUS\tCDS\t91943\t91989\t0.83\t-\t0\ttranscript_id \"g23.t1\"; gene_id \"g23\";\r\n", "scaffold7_cov100\t96787\t96789\tscaffold7_cov100\tAUGUSTUS\tCDS\t96783\t96869\t0.96\t-\t0\ttranscript_id \"g24.t1\"; gene_id \"g24\";\r\n", "scaffold7_cov100\t96787\t96789\tscaffold7_cov100\tAUGUSTUS\tCDS\t96783\t96869\t0.96\t-\t0\ttranscript_id \"g24.t2\"; gene_id \"g24\";\r\n", "scaffold7_cov100\t115927\t115929\tscaffold7_cov100\tAUGUSTUS\tCDS\t115428\t116378\t0.36\t+\t0\ttranscript_id \"g28.t1\"; gene_id \"g28\";\r\n", "scaffold7_cov100\t115931\t115933\tscaffold7_cov100\tAUGUSTUS\tCDS\t115428\t116378\t0.36\t+\t0\ttranscript_id \"g28.t1\"; gene_id \"g28\";\r\n", "scaffold7_cov100\t116068\t116070\tscaffold7_cov100\tAUGUSTUS\tCDS\t115428\t116378\t0.36\t+\t0\ttranscript_id \"g28.t1\"; gene_id \"g28\";\r\n", "\r\n", "==> Meth4_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-unMeth.bed-paCDS <==\r\n", "scaffold6_cov64\t5582\t5583\tscaffold6_cov64\tAUGUSTUS\tCDS\t5583\t5652\t0.26\t-\t0\ttranscript_id \"g1.t1\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t5583\t5585\tscaffold6_cov64\tAUGUSTUS\tCDS\t5583\t5652\t0.26\t-\t0\ttranscript_id \"g1.t1\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t5592\t5594\tscaffold6_cov64\tAUGUSTUS\tCDS\t5583\t5652\t0.26\t-\t0\ttranscript_id \"g1.t1\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t5593\t5594\tscaffold6_cov64\tAUGUSTUS\tCDS\t5594\t5652\t0.54\t-\t0\ttranscript_id \"g1.t2\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t5594\t5596\tscaffold6_cov64\tAUGUSTUS\tCDS\t5583\t5652\t0.26\t-\t0\ttranscript_id \"g1.t1\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t5594\t5596\tscaffold6_cov64\tAUGUSTUS\tCDS\t5594\t5652\t0.54\t-\t0\ttranscript_id \"g1.t2\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t5604\t5606\tscaffold6_cov64\tAUGUSTUS\tCDS\t5583\t5652\t0.26\t-\t0\ttranscript_id \"g1.t1\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t5604\t5606\tscaffold6_cov64\tAUGUSTUS\tCDS\t5594\t5652\t0.54\t-\t0\ttranscript_id \"g1.t2\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t5644\t5646\tscaffold6_cov64\tAUGUSTUS\tCDS\t5583\t5652\t0.26\t-\t0\ttranscript_id \"g1.t1\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t5644\t5646\tscaffold6_cov64\tAUGUSTUS\tCDS\t5594\t5652\t0.54\t-\t0\ttranscript_id \"g1.t2\"; gene_id \"g1\";\r\n", "\r\n", "==> Meth4_R1_001_val_1_bismark_bt2_pe._10x.bedgraph.bed-paCDS <==\r\n", "scaffold6_cov64\t5582\t5583\tscaffold6_cov64\tAUGUSTUS\tCDS\t5583\t5652\t0.26\t-\t0\ttranscript_id \"g1.t1\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t5583\t5585\tscaffold6_cov64\tAUGUSTUS\tCDS\t5583\t5652\t0.26\t-\t0\ttranscript_id \"g1.t1\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t5592\t5594\tscaffold6_cov64\tAUGUSTUS\tCDS\t5583\t5652\t0.26\t-\t0\ttranscript_id \"g1.t1\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t5593\t5594\tscaffold6_cov64\tAUGUSTUS\tCDS\t5594\t5652\t0.54\t-\t0\ttranscript_id \"g1.t2\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t5594\t5596\tscaffold6_cov64\tAUGUSTUS\tCDS\t5583\t5652\t0.26\t-\t0\ttranscript_id \"g1.t1\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t5594\t5596\tscaffold6_cov64\tAUGUSTUS\tCDS\t5594\t5652\t0.54\t-\t0\ttranscript_id \"g1.t2\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t5604\t5606\tscaffold6_cov64\tAUGUSTUS\tCDS\t5583\t5652\t0.26\t-\t0\ttranscript_id \"g1.t1\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t5604\t5606\tscaffold6_cov64\tAUGUSTUS\tCDS\t5594\t5652\t0.54\t-\t0\ttranscript_id \"g1.t2\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t5644\t5646\tscaffold6_cov64\tAUGUSTUS\tCDS\t5583\t5652\t0.26\t-\t0\ttranscript_id \"g1.t1\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t5644\t5646\tscaffold6_cov64\tAUGUSTUS\tCDS\t5594\t5652\t0.54\t-\t0\ttranscript_id \"g1.t2\"; gene_id \"g1\";\r\n", "\r\n", "==> Meth5_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-Meth.bed-paCDS <==\r\n", "scaffold7_cov100\t61080\t61082\tscaffold7_cov100\tAUGUSTUS\tCDS\t61010\t61128\t1\t+\t0\ttranscript_id \"g16.t1\"; gene_id \"g16\";\r\n", "scaffold7_cov100\t96787\t96789\tscaffold7_cov100\tAUGUSTUS\tCDS\t96783\t96869\t0.96\t-\t0\ttranscript_id \"g24.t1\"; gene_id \"g24\";\r\n", "scaffold7_cov100\t96787\t96789\tscaffold7_cov100\tAUGUSTUS\tCDS\t96783\t96869\t0.96\t-\t0\ttranscript_id \"g24.t2\"; gene_id \"g24\";\r\n", "scaffold7_cov100\t96791\t96793\tscaffold7_cov100\tAUGUSTUS\tCDS\t96783\t96869\t0.96\t-\t0\ttranscript_id \"g24.t1\"; gene_id \"g24\";\r\n", "scaffold7_cov100\t96791\t96793\tscaffold7_cov100\tAUGUSTUS\tCDS\t96783\t96869\t0.96\t-\t0\ttranscript_id \"g24.t2\"; gene_id \"g24\";\r\n", "scaffold7_cov100\t96859\t96861\tscaffold7_cov100\tAUGUSTUS\tCDS\t96783\t96869\t0.96\t-\t0\ttranscript_id \"g24.t1\"; gene_id \"g24\";\r\n", "scaffold7_cov100\t96859\t96861\tscaffold7_cov100\tAUGUSTUS\tCDS\t96783\t96869\t0.96\t-\t0\ttranscript_id \"g24.t2\"; gene_id \"g24\";\r\n", "scaffold7_cov100\t204124\t204126\tscaffold7_cov100\tAUGUSTUS\tCDS\t203780\t204500\t0.97\t-\t0\ttranscript_id \"g47.t1\"; gene_id \"g47\";\r\n", "scaffold7_cov100\t204124\t204126\tscaffold7_cov100\tAUGUSTUS\tCDS\t203780\t204500\t0.97\t-\t0\ttranscript_id \"g47.t2\"; gene_id \"g47\";\r\n", "scaffold7_cov100\t338971\t338973\tscaffold7_cov100\tAUGUSTUS\tCDS\t338812\t339072\t1\t+\t0\ttranscript_id \"g74.t1\"; gene_id \"g74\";\r\n", "\r\n", "==> Meth5_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-sparseMeth.bed-paCDS <==\r\n", "scaffold7_cov100\t46343\t46345\tscaffold7_cov100\tAUGUSTUS\tCDS\t45637\t46757\t1\t+\t2\ttranscript_id \"g14.t1\"; gene_id \"g14\";\r\n", "scaffold7_cov100\t94139\t94141\tscaffold7_cov100\tAUGUSTUS\tCDS\t92877\t94547\t1\t-\t1\ttranscript_id \"g24.t1\"; gene_id \"g24\";\r\n", "scaffold7_cov100\t94139\t94141\tscaffold7_cov100\tAUGUSTUS\tCDS\t92877\t94547\t1\t-\t1\ttranscript_id \"g24.t2\"; gene_id \"g24\";\r\n", "scaffold7_cov100\t94142\t94144\tscaffold7_cov100\tAUGUSTUS\tCDS\t92877\t94547\t1\t-\t1\ttranscript_id \"g24.t1\"; gene_id \"g24\";\r\n", "scaffold7_cov100\t94142\t94144\tscaffold7_cov100\tAUGUSTUS\tCDS\t92877\t94547\t1\t-\t1\ttranscript_id \"g24.t2\"; gene_id \"g24\";\r\n", "scaffold7_cov100\t94939\t94941\tscaffold7_cov100\tAUGUSTUS\tCDS\t94906\t94950\t0.9\t-\t1\ttranscript_id \"g24.t1\"; gene_id \"g24\";\r\n", "scaffold7_cov100\t94939\t94941\tscaffold7_cov100\tAUGUSTUS\tCDS\t94906\t94950\t0.9\t-\t1\ttranscript_id \"g24.t2\"; gene_id \"g24\";\r\n", "scaffold7_cov100\t131174\t131176\tscaffold7_cov100\tAUGUSTUS\tCDS\t131111\t131291\t1\t+\t1\ttranscript_id \"g31.t1\"; gene_id \"g31\";\r\n", "scaffold7_cov100\t131174\t131176\tscaffold7_cov100\tAUGUSTUS\tCDS\t131111\t131291\t1\t+\t1\ttranscript_id \"g31.t2\"; gene_id \"g31\";\r\n", "scaffold7_cov100\t236368\t236370\tscaffold7_cov100\tAUGUSTUS\tCDS\t236352\t236464\t0.86\t-\t2\ttranscript_id \"g51.t1\"; gene_id \"g51\";\r\n", "\r\n", "==> Meth5_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-unMeth.bed-paCDS <==\r\n", "scaffold6_cov64\t5582\t5583\tscaffold6_cov64\tAUGUSTUS\tCDS\t5583\t5652\t0.26\t-\t0\ttranscript_id \"g1.t1\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t5583\t5585\tscaffold6_cov64\tAUGUSTUS\tCDS\t5583\t5652\t0.26\t-\t0\ttranscript_id \"g1.t1\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t5592\t5594\tscaffold6_cov64\tAUGUSTUS\tCDS\t5583\t5652\t0.26\t-\t0\ttranscript_id \"g1.t1\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t5593\t5594\tscaffold6_cov64\tAUGUSTUS\tCDS\t5594\t5652\t0.54\t-\t0\ttranscript_id \"g1.t2\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t5594\t5596\tscaffold6_cov64\tAUGUSTUS\tCDS\t5583\t5652\t0.26\t-\t0\ttranscript_id \"g1.t1\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t5594\t5596\tscaffold6_cov64\tAUGUSTUS\tCDS\t5594\t5652\t0.54\t-\t0\ttranscript_id \"g1.t2\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t5604\t5606\tscaffold6_cov64\tAUGUSTUS\tCDS\t5583\t5652\t0.26\t-\t0\ttranscript_id \"g1.t1\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t5604\t5606\tscaffold6_cov64\tAUGUSTUS\tCDS\t5594\t5652\t0.54\t-\t0\ttranscript_id \"g1.t2\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t5644\t5646\tscaffold6_cov64\tAUGUSTUS\tCDS\t5583\t5652\t0.26\t-\t0\ttranscript_id \"g1.t1\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t5644\t5646\tscaffold6_cov64\tAUGUSTUS\tCDS\t5594\t5652\t0.54\t-\t0\ttranscript_id \"g1.t2\"; gene_id \"g1\";\r\n", "\r\n", "==> Meth5_R1_001_val_1_bismark_bt2_pe._10x.bedgraph.bed-paCDS <==\r\n", "scaffold6_cov64\t5582\t5583\tscaffold6_cov64\tAUGUSTUS\tCDS\t5583\t5652\t0.26\t-\t0\ttranscript_id \"g1.t1\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t5583\t5585\tscaffold6_cov64\tAUGUSTUS\tCDS\t5583\t5652\t0.26\t-\t0\ttranscript_id \"g1.t1\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t5592\t5594\tscaffold6_cov64\tAUGUSTUS\tCDS\t5583\t5652\t0.26\t-\t0\ttranscript_id \"g1.t1\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t5593\t5594\tscaffold6_cov64\tAUGUSTUS\tCDS\t5594\t5652\t0.54\t-\t0\ttranscript_id \"g1.t2\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t5594\t5596\tscaffold6_cov64\tAUGUSTUS\tCDS\t5583\t5652\t0.26\t-\t0\ttranscript_id \"g1.t1\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t5594\t5596\tscaffold6_cov64\tAUGUSTUS\tCDS\t5594\t5652\t0.54\t-\t0\ttranscript_id \"g1.t2\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t5604\t5606\tscaffold6_cov64\tAUGUSTUS\tCDS\t5583\t5652\t0.26\t-\t0\ttranscript_id \"g1.t1\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t5604\t5606\tscaffold6_cov64\tAUGUSTUS\tCDS\t5594\t5652\t0.54\t-\t0\ttranscript_id \"g1.t2\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t5644\t5646\tscaffold6_cov64\tAUGUSTUS\tCDS\t5583\t5652\t0.26\t-\t0\ttranscript_id \"g1.t1\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t5644\t5646\tscaffold6_cov64\tAUGUSTUS\tCDS\t5594\t5652\t0.54\t-\t0\ttranscript_id \"g1.t2\"; gene_id \"g1\";\r\n", "\r\n", "==> Meth6_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-Meth.bed-paCDS <==\r\n", "scaffold7_cov100\t346786\t346788\tscaffold7_cov100\tAUGUSTUS\tCDS\t346473\t346845\t1\t+\t0\ttranscript_id \"g78.t1\"; gene_id \"g78\";\r\n", "scaffold7_cov100\t346786\t346788\tscaffold7_cov100\tAUGUSTUS\tCDS\t346473\t346845\t1\t+\t0\ttranscript_id \"g78.t2\"; gene_id \"g78\";\r\n", "scaffold7_cov100\t360165\t360167\tscaffold7_cov100\tAUGUSTUS\tCDS\t359591\t360506\t0.93\t-\t1\ttranscript_id \"g79.t1\"; gene_id \"g79\";\r\n", "scaffold7_cov100\t360165\t360167\tscaffold7_cov100\tAUGUSTUS\tCDS\t359591\t360506\t0.93\t-\t1\ttranscript_id \"g79.t2\"; gene_id \"g79\";\r\n", "scaffold7_cov100\t386815\t386817\tscaffold7_cov100\tAUGUSTUS\tCDS\t386292\t387086\t0.59\t+\t0\ttranscript_id \"g84.t1\"; gene_id \"g84\";\r\n", "scaffold7_cov100\t386817\t386819\tscaffold7_cov100\tAUGUSTUS\tCDS\t386292\t387086\t0.59\t+\t0\ttranscript_id \"g84.t1\"; gene_id \"g84\";\r\n", "scaffold7_cov100\t403347\t403349\tscaffold7_cov100\tAUGUSTUS\tCDS\t403291\t403478\t1\t+\t0\ttranscript_id \"g87.t1\"; gene_id \"g87\";\r\n", "scaffold7_cov100\t403347\t403349\tscaffold7_cov100\tAUGUSTUS\tCDS\t403291\t403478\t1\t+\t0\ttranscript_id \"g87.t2\"; gene_id \"g87\";\r\n", "scaffold7_cov100\t403727\t403729\tscaffold7_cov100\tAUGUSTUS\tCDS\t403652\t403885\t1\t+\t1\ttranscript_id \"g87.t1\"; gene_id \"g87\";\r\n", "scaffold7_cov100\t403727\t403729\tscaffold7_cov100\tAUGUSTUS\tCDS\t403652\t403885\t1\t+\t1\ttranscript_id \"g87.t2\"; gene_id \"g87\";\r\n", "\r\n", "==> Meth6_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-sparseMeth.bed-paCDS <==\r\n", "scaffold6_cov64\t5604\t5606\tscaffold6_cov64\tAUGUSTUS\tCDS\t5583\t5652\t0.26\t-\t0\ttranscript_id \"g1.t1\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t5604\t5606\tscaffold6_cov64\tAUGUSTUS\tCDS\t5594\t5652\t0.54\t-\t0\ttranscript_id \"g1.t2\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t6266\t6267\tscaffold6_cov64\tAUGUSTUS\tCDS\t5946\t6267\t0.33\t+\t2\ttranscript_id \"g2.t1\"; gene_id \"g2\";\r\n", "scaffold6_cov64\t6266\t6267\tscaffold6_cov64\tAUGUSTUS\tCDS\t5982\t6267\t0.27\t+\t2\ttranscript_id \"g2.t2\"; gene_id \"g2\";\r\n", "scaffold7_cov100\t32984\t32986\tscaffold7_cov100\tAUGUSTUS\tCDS\t32892\t33408\t1\t-\t0\ttranscript_id \"g13.t1\"; gene_id \"g13\";\r\n", "scaffold7_cov100\t32984\t32986\tscaffold7_cov100\tAUGUSTUS\tCDS\t32892\t33408\t1\t-\t0\ttranscript_id \"g13.t2\"; gene_id \"g13\";\r\n", "scaffold7_cov100\t46343\t46345\tscaffold7_cov100\tAUGUSTUS\tCDS\t45637\t46757\t1\t+\t2\ttranscript_id \"g14.t1\"; gene_id \"g14\";\r\n", "scaffold7_cov100\t61080\t61082\tscaffold7_cov100\tAUGUSTUS\tCDS\t61010\t61128\t1\t+\t0\ttranscript_id \"g16.t1\"; gene_id \"g16\";\r\n", "scaffold7_cov100\t118348\t118350\tscaffold7_cov100\tAUGUSTUS\tCDS\t118239\t118350\t1\t+\t0\ttranscript_id \"g30.t1\"; gene_id \"g30\";\r\n", "scaffold7_cov100\t151954\t151956\tscaffold7_cov100\tAUGUSTUS\tCDS\t151749\t152078\t0.64\t+\t0\ttranscript_id \"g40.t1\"; gene_id \"g40\";\r\n", "\r\n", "==> Meth6_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-unMeth.bed-paCDS <==\r\n", "scaffold6_cov64\t5582\t5583\tscaffold6_cov64\tAUGUSTUS\tCDS\t5583\t5652\t0.26\t-\t0\ttranscript_id \"g1.t1\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t5583\t5585\tscaffold6_cov64\tAUGUSTUS\tCDS\t5583\t5652\t0.26\t-\t0\ttranscript_id \"g1.t1\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t5592\t5594\tscaffold6_cov64\tAUGUSTUS\tCDS\t5583\t5652\t0.26\t-\t0\ttranscript_id \"g1.t1\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t5593\t5594\tscaffold6_cov64\tAUGUSTUS\tCDS\t5594\t5652\t0.54\t-\t0\ttranscript_id \"g1.t2\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t5594\t5596\tscaffold6_cov64\tAUGUSTUS\tCDS\t5583\t5652\t0.26\t-\t0\ttranscript_id \"g1.t1\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t5594\t5596\tscaffold6_cov64\tAUGUSTUS\tCDS\t5594\t5652\t0.54\t-\t0\ttranscript_id \"g1.t2\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t5644\t5646\tscaffold6_cov64\tAUGUSTUS\tCDS\t5583\t5652\t0.26\t-\t0\ttranscript_id \"g1.t1\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t5644\t5646\tscaffold6_cov64\tAUGUSTUS\tCDS\t5594\t5652\t0.54\t-\t0\ttranscript_id \"g1.t2\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t5821\t5823\tscaffold6_cov64\tAUGUSTUS\tCDS\t5805\t5838\t0.98\t+\t0\ttranscript_id \"g2.t1\"; gene_id \"g2\";\r\n", "scaffold6_cov64\t5821\t5823\tscaffold6_cov64\tAUGUSTUS\tCDS\t5805\t5838\t0.98\t+\t0\ttranscript_id \"g2.t2\"; gene_id \"g2\";\r\n", "\r\n", "==> Meth6_R1_001_val_1_bismark_bt2_pe._10x.bedgraph.bed-paCDS <==\r\n", "scaffold6_cov64\t5582\t5583\tscaffold6_cov64\tAUGUSTUS\tCDS\t5583\t5652\t0.26\t-\t0\ttranscript_id \"g1.t1\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t5583\t5585\tscaffold6_cov64\tAUGUSTUS\tCDS\t5583\t5652\t0.26\t-\t0\ttranscript_id \"g1.t1\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t5592\t5594\tscaffold6_cov64\tAUGUSTUS\tCDS\t5583\t5652\t0.26\t-\t0\ttranscript_id \"g1.t1\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t5593\t5594\tscaffold6_cov64\tAUGUSTUS\tCDS\t5594\t5652\t0.54\t-\t0\ttranscript_id \"g1.t2\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t5594\t5596\tscaffold6_cov64\tAUGUSTUS\tCDS\t5583\t5652\t0.26\t-\t0\ttranscript_id \"g1.t1\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t5594\t5596\tscaffold6_cov64\tAUGUSTUS\tCDS\t5594\t5652\t0.54\t-\t0\ttranscript_id \"g1.t2\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t5604\t5606\tscaffold6_cov64\tAUGUSTUS\tCDS\t5583\t5652\t0.26\t-\t0\ttranscript_id \"g1.t1\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t5604\t5606\tscaffold6_cov64\tAUGUSTUS\tCDS\t5594\t5652\t0.54\t-\t0\ttranscript_id \"g1.t2\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t5644\t5646\tscaffold6_cov64\tAUGUSTUS\tCDS\t5583\t5652\t0.26\t-\t0\ttranscript_id \"g1.t1\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t5644\t5646\tscaffold6_cov64\tAUGUSTUS\tCDS\t5594\t5652\t0.54\t-\t0\ttranscript_id \"g1.t2\"; gene_id \"g1\";\r\n", "\r\n", "==> Meth7_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-Meth.bed-paCDS <==\r\n", "scaffold7_cov100\t5500\t5502\tscaffold7_cov100\tAUGUSTUS\tCDS\t5466\t5540\t1\t-\t2\ttranscript_id \"g4.t1\"; gene_id \"g4\";\r\n", "scaffold7_cov100\t5500\t5502\tscaffold7_cov100\tAUGUSTUS\tCDS\t5466\t5540\t1\t-\t2\ttranscript_id \"g4.t2\"; gene_id \"g4\";\r\n", "scaffold7_cov100\t6144\t6146\tscaffold7_cov100\tAUGUSTUS\tCDS\t6091\t6217\t0.48\t-\t0\ttranscript_id \"g4.t1\"; gene_id \"g4\";\r\n", "scaffold7_cov100\t6144\t6146\tscaffold7_cov100\tAUGUSTUS\tCDS\t6091\t6211\t0.52\t-\t0\ttranscript_id \"g4.t2\"; gene_id \"g4\";\r\n", "scaffold7_cov100\t6188\t6190\tscaffold7_cov100\tAUGUSTUS\tCDS\t6091\t6217\t0.48\t-\t0\ttranscript_id \"g4.t1\"; gene_id \"g4\";\r\n", "scaffold7_cov100\t6188\t6190\tscaffold7_cov100\tAUGUSTUS\tCDS\t6091\t6211\t0.52\t-\t0\ttranscript_id \"g4.t2\"; gene_id \"g4\";\r\n", "scaffold7_cov100\t6198\t6200\tscaffold7_cov100\tAUGUSTUS\tCDS\t6091\t6217\t0.48\t-\t0\ttranscript_id \"g4.t1\"; gene_id \"g4\";\r\n", "scaffold7_cov100\t6198\t6200\tscaffold7_cov100\tAUGUSTUS\tCDS\t6091\t6211\t0.52\t-\t0\ttranscript_id \"g4.t2\"; gene_id \"g4\";\r\n", "scaffold7_cov100\t7696\t7698\tscaffold7_cov100\tAUGUSTUS\tCDS\t7650\t7715\t1\t-\t2\ttranscript_id \"g5.t1\"; gene_id \"g5\";\r\n", "scaffold7_cov100\t7696\t7698\tscaffold7_cov100\tAUGUSTUS\tCDS\t7650\t7715\t1\t-\t2\ttranscript_id \"g5.t2\"; gene_id \"g5\";\r\n", "\r\n", "==> Meth7_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-sparseMeth.bed-paCDS <==\r\n", "scaffold7_cov100\t2080\t2082\tscaffold7_cov100\tAUGUSTUS\tCDS\t1\t2566\t0.96\t+\t1\ttranscript_id \"g3.t1\"; gene_id \"g3\";\r\n", "scaffold7_cov100\t14042\t14044\tscaffold7_cov100\tAUGUSTUS\tCDS\t13744\t14512\t1\t-\t0\ttranscript_id \"g7.t1\"; gene_id \"g7\";\r\n", "scaffold7_cov100\t17952\t17954\tscaffold7_cov100\tAUGUSTUS\tCDS\t15738\t18320\t0.53\t+\t0\ttranscript_id \"g8.t1\"; gene_id \"g8\";\r\n", "scaffold7_cov100\t17952\t17954\tscaffold7_cov100\tAUGUSTUS\tCDS\t15789\t18320\t0.43\t+\t0\ttranscript_id \"g8.t2\"; gene_id \"g8\";\r\n", "scaffold7_cov100\t19493\t19495\tscaffold7_cov100\tAUGUSTUS\tCDS\t19312\t19534\t0.29\t+\t0\ttranscript_id \"g10.t1\"; gene_id \"g10\";\r\n", "scaffold7_cov100\t19493\t19495\tscaffold7_cov100\tAUGUSTUS\tCDS\t19336\t19534\t0.59\t+\t0\ttranscript_id \"g10.t2\"; gene_id \"g10\";\r\n", "scaffold7_cov100\t52752\t52754\tscaffold7_cov100\tAUGUSTUS\tCDS\t52729\t52811\t1\t+\t2\ttranscript_id \"g16.t1\"; gene_id \"g16\";\r\n", "scaffold7_cov100\t66986\t66988\tscaffold7_cov100\tAUGUSTUS\tCDS\t66872\t67198\t1\t-\t2\ttranscript_id \"g17.t1\"; gene_id \"g17\";\r\n", "scaffold7_cov100\t68605\t68607\tscaffold7_cov100\tAUGUSTUS\tCDS\t68550\t68618\t1\t-\t2\ttranscript_id \"g18.t1\"; gene_id \"g18\";\r\n", "scaffold7_cov100\t131174\t131176\tscaffold7_cov100\tAUGUSTUS\tCDS\t131111\t131291\t1\t+\t1\ttranscript_id \"g31.t1\"; gene_id \"g31\";\r\n", "\r\n", "==> Meth7_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-unMeth.bed-paCDS <==\r\n", "scaffold6_cov64\t5821\t5823\tscaffold6_cov64\tAUGUSTUS\tCDS\t5805\t5838\t0.98\t+\t0\ttranscript_id \"g2.t1\"; gene_id \"g2\";\r\n", "scaffold6_cov64\t5821\t5823\tscaffold6_cov64\tAUGUSTUS\tCDS\t5805\t5838\t0.98\t+\t0\ttranscript_id \"g2.t2\"; gene_id \"g2\";\r\n", "scaffold6_cov64\t6183\t6185\tscaffold6_cov64\tAUGUSTUS\tCDS\t5946\t6267\t0.33\t+\t2\ttranscript_id \"g2.t1\"; gene_id \"g2\";\r\n", "scaffold6_cov64\t6183\t6185\tscaffold6_cov64\tAUGUSTUS\tCDS\t5982\t6267\t0.27\t+\t2\ttranscript_id \"g2.t2\"; gene_id \"g2\";\r\n", "scaffold6_cov64\t6186\t6188\tscaffold6_cov64\tAUGUSTUS\tCDS\t5946\t6267\t0.33\t+\t2\ttranscript_id \"g2.t1\"; gene_id \"g2\";\r\n", "scaffold6_cov64\t6186\t6188\tscaffold6_cov64\tAUGUSTUS\tCDS\t5982\t6267\t0.27\t+\t2\ttranscript_id \"g2.t2\"; gene_id \"g2\";\r\n", "scaffold6_cov64\t6194\t6196\tscaffold6_cov64\tAUGUSTUS\tCDS\t5946\t6267\t0.33\t+\t2\ttranscript_id \"g2.t1\"; gene_id \"g2\";\r\n", "scaffold6_cov64\t6194\t6196\tscaffold6_cov64\tAUGUSTUS\tCDS\t5982\t6267\t0.27\t+\t2\ttranscript_id \"g2.t2\"; gene_id \"g2\";\r\n", "scaffold6_cov64\t6266\t6267\tscaffold6_cov64\tAUGUSTUS\tCDS\t5946\t6267\t0.33\t+\t2\ttranscript_id \"g2.t1\"; gene_id \"g2\";\r\n", "scaffold6_cov64\t6266\t6267\tscaffold6_cov64\tAUGUSTUS\tCDS\t5982\t6267\t0.27\t+\t2\ttranscript_id \"g2.t2\"; gene_id \"g2\";\r\n", "\r\n", "==> Meth7_R1_001_val_1_bismark_bt2_pe._10x.bedgraph.bed-paCDS <==\r\n", "scaffold6_cov64\t5821\t5823\tscaffold6_cov64\tAUGUSTUS\tCDS\t5805\t5838\t0.98\t+\t0\ttranscript_id \"g2.t1\"; gene_id \"g2\";\r\n", "scaffold6_cov64\t5821\t5823\tscaffold6_cov64\tAUGUSTUS\tCDS\t5805\t5838\t0.98\t+\t0\ttranscript_id \"g2.t2\"; gene_id \"g2\";\r\n", "scaffold6_cov64\t6183\t6185\tscaffold6_cov64\tAUGUSTUS\tCDS\t5946\t6267\t0.33\t+\t2\ttranscript_id \"g2.t1\"; gene_id \"g2\";\r\n", "scaffold6_cov64\t6183\t6185\tscaffold6_cov64\tAUGUSTUS\tCDS\t5982\t6267\t0.27\t+\t2\ttranscript_id \"g2.t2\"; gene_id \"g2\";\r\n", "scaffold6_cov64\t6186\t6188\tscaffold6_cov64\tAUGUSTUS\tCDS\t5946\t6267\t0.33\t+\t2\ttranscript_id \"g2.t1\"; gene_id \"g2\";\r\n", "scaffold6_cov64\t6186\t6188\tscaffold6_cov64\tAUGUSTUS\tCDS\t5982\t6267\t0.27\t+\t2\ttranscript_id \"g2.t2\"; gene_id \"g2\";\r\n", "scaffold6_cov64\t6194\t6196\tscaffold6_cov64\tAUGUSTUS\tCDS\t5946\t6267\t0.33\t+\t2\ttranscript_id \"g2.t1\"; gene_id \"g2\";\r\n", "scaffold6_cov64\t6194\t6196\tscaffold6_cov64\tAUGUSTUS\tCDS\t5982\t6267\t0.27\t+\t2\ttranscript_id \"g2.t2\"; gene_id \"g2\";\r\n", "scaffold6_cov64\t6266\t6267\tscaffold6_cov64\tAUGUSTUS\tCDS\t5946\t6267\t0.33\t+\t2\ttranscript_id \"g2.t1\"; gene_id \"g2\";\r\n", "scaffold6_cov64\t6266\t6267\tscaffold6_cov64\tAUGUSTUS\tCDS\t5982\t6267\t0.27\t+\t2\ttranscript_id \"g2.t2\"; gene_id \"g2\";\r\n", "\r\n", "==> Meth8_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-Meth.bed-paCDS <==\r\n", "scaffold7_cov100\t6144\t6146\tscaffold7_cov100\tAUGUSTUS\tCDS\t6091\t6217\t0.48\t-\t0\ttranscript_id \"g4.t1\"; gene_id \"g4\";\r\n", "scaffold7_cov100\t6144\t6146\tscaffold7_cov100\tAUGUSTUS\tCDS\t6091\t6211\t0.52\t-\t0\ttranscript_id \"g4.t2\"; gene_id \"g4\";\r\n", "scaffold7_cov100\t6188\t6190\tscaffold7_cov100\tAUGUSTUS\tCDS\t6091\t6217\t0.48\t-\t0\ttranscript_id \"g4.t1\"; gene_id \"g4\";\r\n", "scaffold7_cov100\t6188\t6190\tscaffold7_cov100\tAUGUSTUS\tCDS\t6091\t6211\t0.52\t-\t0\ttranscript_id \"g4.t2\"; gene_id \"g4\";\r\n", "scaffold7_cov100\t6198\t6200\tscaffold7_cov100\tAUGUSTUS\tCDS\t6091\t6217\t0.48\t-\t0\ttranscript_id \"g4.t1\"; gene_id \"g4\";\r\n", "scaffold7_cov100\t6198\t6200\tscaffold7_cov100\tAUGUSTUS\tCDS\t6091\t6211\t0.52\t-\t0\ttranscript_id \"g4.t2\"; gene_id \"g4\";\r\n", "scaffold7_cov100\t7892\t7893\tscaffold7_cov100\tAUGUSTUS\tCDS\t7893\t7980\t1\t-\t0\ttranscript_id \"g5.t1\"; gene_id \"g5\";\r\n", "scaffold7_cov100\t7892\t7893\tscaffold7_cov100\tAUGUSTUS\tCDS\t7893\t7980\t1\t-\t0\ttranscript_id \"g5.t2\"; gene_id \"g5\";\r\n", "scaffold7_cov100\t16831\t16833\tscaffold7_cov100\tAUGUSTUS\tCDS\t15738\t18320\t0.53\t+\t0\ttranscript_id \"g8.t1\"; gene_id \"g8\";\r\n", "scaffold7_cov100\t16831\t16833\tscaffold7_cov100\tAUGUSTUS\tCDS\t15789\t18320\t0.43\t+\t0\ttranscript_id \"g8.t2\"; gene_id \"g8\";\r\n", "\r\n", "==> Meth8_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-sparseMeth.bed-paCDS <==\r\n", "scaffold7_cov100\t5500\t5502\tscaffold7_cov100\tAUGUSTUS\tCDS\t5466\t5540\t1\t-\t2\ttranscript_id \"g4.t1\"; gene_id \"g4\";\r\n", "scaffold7_cov100\t5500\t5502\tscaffold7_cov100\tAUGUSTUS\tCDS\t5466\t5540\t1\t-\t2\ttranscript_id \"g4.t2\"; gene_id \"g4\";\r\n", "scaffold7_cov100\t131221\t131223\tscaffold7_cov100\tAUGUSTUS\tCDS\t131111\t131291\t1\t+\t1\ttranscript_id \"g31.t1\"; gene_id \"g31\";\r\n", "scaffold7_cov100\t131221\t131223\tscaffold7_cov100\tAUGUSTUS\tCDS\t131111\t131291\t1\t+\t1\ttranscript_id \"g31.t2\"; gene_id \"g31\";\r\n", "scaffold7_cov100\t131255\t131257\tscaffold7_cov100\tAUGUSTUS\tCDS\t131111\t131291\t1\t+\t1\ttranscript_id \"g31.t1\"; gene_id \"g31\";\r\n", "scaffold7_cov100\t131255\t131257\tscaffold7_cov100\tAUGUSTUS\tCDS\t131111\t131291\t1\t+\t1\ttranscript_id \"g31.t2\"; gene_id \"g31\";\r\n", "scaffold7_cov100\t470212\t470214\tscaffold7_cov100\tAUGUSTUS\tCDS\t470160\t470382\t1\t+\t2\ttranscript_id \"g103.t1\"; gene_id \"g103\";\r\n", "scaffold7_cov100\t470966\t470968\tscaffold7_cov100\tAUGUSTUS\tCDS\t470889\t471265\t1\t+\t1\ttranscript_id \"g103.t1\"; gene_id \"g103\";\r\n", "scaffold7_cov100\t471533\t471535\tscaffold7_cov100\tAUGUSTUS\tCDS\t471431\t471862\t1\t+\t2\ttranscript_id \"g103.t1\"; gene_id \"g103\";\r\n", "scaffold21_cov102\t86899\t86901\tscaffold21_cov102\tAUGUSTUS\tCDS\t86855\t86946\t0.67\t+\t2\ttranscript_id \"g235.t1\"; gene_id \"g235\";\r\n", "\r\n", "==> Meth8_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-unMeth.bed-paCDS <==\r\n", "scaffold7_cov100\t17164\t17166\tscaffold7_cov100\tAUGUSTUS\tCDS\t15738\t18320\t0.53\t+\t0\ttranscript_id \"g8.t1\"; gene_id \"g8\";\r\n", "scaffold7_cov100\t17164\t17166\tscaffold7_cov100\tAUGUSTUS\tCDS\t15789\t18320\t0.43\t+\t0\ttranscript_id \"g8.t2\"; gene_id \"g8\";\r\n", "scaffold7_cov100\t46203\t46205\tscaffold7_cov100\tAUGUSTUS\tCDS\t45637\t46757\t1\t+\t2\ttranscript_id \"g14.t1\"; gene_id \"g14\";\r\n", "scaffold7_cov100\t46206\t46208\tscaffold7_cov100\tAUGUSTUS\tCDS\t45637\t46757\t1\t+\t2\ttranscript_id \"g14.t1\"; gene_id \"g14\";\r\n", "scaffold7_cov100\t46231\t46233\tscaffold7_cov100\tAUGUSTUS\tCDS\t45637\t46757\t1\t+\t2\ttranscript_id \"g14.t1\"; gene_id \"g14\";\r\n", "scaffold7_cov100\t77629\t77631\tscaffold7_cov100\tAUGUSTUS\tCDS\t77522\t77701\t1\t-\t0\ttranscript_id \"g20.t1\"; gene_id \"g20\";\r\n", "scaffold7_cov100\t269392\t269394\tscaffold7_cov100\tAUGUSTUS\tCDS\t269353\t269846\t1\t-\t0\ttranscript_id \"g56.t1\"; gene_id \"g56\";\r\n", "scaffold7_cov100\t269542\t269544\tscaffold7_cov100\tAUGUSTUS\tCDS\t269353\t269846\t1\t-\t0\ttranscript_id \"g56.t1\"; gene_id \"g56\";\r\n", "scaffold7_cov100\t269713\t269715\tscaffold7_cov100\tAUGUSTUS\tCDS\t269353\t269846\t1\t-\t0\ttranscript_id \"g56.t1\"; gene_id \"g56\";\r\n", "scaffold7_cov100\t403747\t403749\tscaffold7_cov100\tAUGUSTUS\tCDS\t403652\t403885\t1\t+\t1\ttranscript_id \"g87.t1\"; gene_id \"g87\";\r\n", "\r\n", "==> Meth8_R1_001_val_1_bismark_bt2_pe._10x.bedgraph.bed-paCDS <==\r\n", "scaffold7_cov100\t5500\t5502\tscaffold7_cov100\tAUGUSTUS\tCDS\t5466\t5540\t1\t-\t2\ttranscript_id \"g4.t1\"; gene_id \"g4\";\r\n", "scaffold7_cov100\t5500\t5502\tscaffold7_cov100\tAUGUSTUS\tCDS\t5466\t5540\t1\t-\t2\ttranscript_id \"g4.t2\"; gene_id \"g4\";\r\n", "scaffold7_cov100\t6144\t6146\tscaffold7_cov100\tAUGUSTUS\tCDS\t6091\t6217\t0.48\t-\t0\ttranscript_id \"g4.t1\"; gene_id \"g4\";\r\n", "scaffold7_cov100\t6144\t6146\tscaffold7_cov100\tAUGUSTUS\tCDS\t6091\t6211\t0.52\t-\t0\ttranscript_id \"g4.t2\"; gene_id \"g4\";\r\n", "scaffold7_cov100\t6188\t6190\tscaffold7_cov100\tAUGUSTUS\tCDS\t6091\t6217\t0.48\t-\t0\ttranscript_id \"g4.t1\"; gene_id \"g4\";\r\n", "scaffold7_cov100\t6188\t6190\tscaffold7_cov100\tAUGUSTUS\tCDS\t6091\t6211\t0.52\t-\t0\ttranscript_id \"g4.t2\"; gene_id \"g4\";\r\n", "scaffold7_cov100\t6198\t6200\tscaffold7_cov100\tAUGUSTUS\tCDS\t6091\t6217\t0.48\t-\t0\ttranscript_id \"g4.t1\"; gene_id \"g4\";\r\n", "scaffold7_cov100\t6198\t6200\tscaffold7_cov100\tAUGUSTUS\tCDS\t6091\t6211\t0.52\t-\t0\ttranscript_id \"g4.t2\"; gene_id \"g4\";\r\n", "scaffold7_cov100\t7892\t7893\tscaffold7_cov100\tAUGUSTUS\tCDS\t7893\t7980\t1\t-\t0\ttranscript_id \"g5.t1\"; gene_id \"g5\";\r\n", "scaffold7_cov100\t7892\t7893\tscaffold7_cov100\tAUGUSTUS\tCDS\t7893\t7980\t1\t-\t0\ttranscript_id \"g5.t2\"; gene_id \"g5\";\r\n", "\r\n", "==> Meth9_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-Meth.bed-paCDS <==\r\n", "scaffold7_cov100\t6144\t6146\tscaffold7_cov100\tAUGUSTUS\tCDS\t6091\t6217\t0.48\t-\t0\ttranscript_id \"g4.t1\"; gene_id \"g4\";\r\n", "scaffold7_cov100\t6144\t6146\tscaffold7_cov100\tAUGUSTUS\tCDS\t6091\t6211\t0.52\t-\t0\ttranscript_id \"g4.t2\"; gene_id \"g4\";\r\n", "scaffold7_cov100\t6188\t6190\tscaffold7_cov100\tAUGUSTUS\tCDS\t6091\t6217\t0.48\t-\t0\ttranscript_id \"g4.t1\"; gene_id \"g4\";\r\n", "scaffold7_cov100\t6188\t6190\tscaffold7_cov100\tAUGUSTUS\tCDS\t6091\t6211\t0.52\t-\t0\ttranscript_id \"g4.t2\"; gene_id \"g4\";\r\n", "scaffold7_cov100\t6198\t6200\tscaffold7_cov100\tAUGUSTUS\tCDS\t6091\t6217\t0.48\t-\t0\ttranscript_id \"g4.t1\"; gene_id \"g4\";\r\n", "scaffold7_cov100\t6198\t6200\tscaffold7_cov100\tAUGUSTUS\tCDS\t6091\t6211\t0.52\t-\t0\ttranscript_id \"g4.t2\"; gene_id \"g4\";\r\n", "scaffold7_cov100\t7696\t7698\tscaffold7_cov100\tAUGUSTUS\tCDS\t7650\t7715\t1\t-\t2\ttranscript_id \"g5.t1\"; gene_id \"g5\";\r\n", "scaffold7_cov100\t7696\t7698\tscaffold7_cov100\tAUGUSTUS\tCDS\t7650\t7715\t1\t-\t2\ttranscript_id \"g5.t2\"; gene_id \"g5\";\r\n", "scaffold7_cov100\t7892\t7893\tscaffold7_cov100\tAUGUSTUS\tCDS\t7893\t7980\t1\t-\t0\ttranscript_id \"g5.t1\"; gene_id \"g5\";\r\n", "scaffold7_cov100\t7892\t7893\tscaffold7_cov100\tAUGUSTUS\tCDS\t7893\t7980\t1\t-\t0\ttranscript_id \"g5.t2\"; gene_id \"g5\";\r\n", "\r\n", "==> Meth9_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-sparseMeth.bed-paCDS <==\r\n", "scaffold7_cov100\t10755\t10757\tscaffold7_cov100\tAUGUSTUS\tCDS\t10595\t10789\t0.95\t-\t0\ttranscript_id \"g6.t1\"; gene_id \"g6\";\r\n", "scaffold7_cov100\t14042\t14044\tscaffold7_cov100\tAUGUSTUS\tCDS\t13744\t14512\t1\t-\t0\ttranscript_id \"g7.t1\"; gene_id \"g7\";\r\n", "scaffold7_cov100\t17952\t17954\tscaffold7_cov100\tAUGUSTUS\tCDS\t15738\t18320\t0.53\t+\t0\ttranscript_id \"g8.t1\"; gene_id \"g8\";\r\n", "scaffold7_cov100\t17952\t17954\tscaffold7_cov100\tAUGUSTUS\tCDS\t15789\t18320\t0.43\t+\t0\ttranscript_id \"g8.t2\"; gene_id \"g8\";\r\n", "scaffold7_cov100\t20473\t20475\tscaffold7_cov100\tAUGUSTUS\tCDS\t20394\t20696\t0.71\t+\t0\ttranscript_id \"g11.t1\"; gene_id \"g11\";\r\n", "scaffold7_cov100\t46359\t46361\tscaffold7_cov100\tAUGUSTUS\tCDS\t45637\t46757\t1\t+\t2\ttranscript_id \"g14.t1\"; gene_id \"g14\";\r\n", "scaffold7_cov100\t75788\t75790\tscaffold7_cov100\tAUGUSTUS\tCDS\t75730\t75808\t1\t-\t0\ttranscript_id \"g19.t1\"; gene_id \"g19\";\r\n", "scaffold7_cov100\t114510\t114512\tscaffold7_cov100\tAUGUSTUS\tCDS\t114378\t114581\t0.65\t-\t0\ttranscript_id \"g29.t1\"; gene_id \"g29\";\r\n", "scaffold7_cov100\t131221\t131223\tscaffold7_cov100\tAUGUSTUS\tCDS\t131111\t131291\t1\t+\t1\ttranscript_id \"g31.t1\"; gene_id \"g31\";\r\n", "scaffold7_cov100\t131221\t131223\tscaffold7_cov100\tAUGUSTUS\tCDS\t131111\t131291\t1\t+\t1\ttranscript_id \"g31.t2\"; gene_id \"g31\";\r\n", "\r\n", "==> Meth9_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-unMeth.bed-paCDS <==\r\n", "scaffold6_cov64\t2179\t2181\tscaffold6_cov64\tAUGUSTUS\tCDS\t1922\t2269\t1\t-\t2\ttranscript_id \"g1.t1\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t2179\t2181\tscaffold6_cov64\tAUGUSTUS\tCDS\t1922\t2269\t1\t-\t2\ttranscript_id \"g1.t2\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t5582\t5583\tscaffold6_cov64\tAUGUSTUS\tCDS\t5583\t5652\t0.26\t-\t0\ttranscript_id \"g1.t1\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t5583\t5585\tscaffold6_cov64\tAUGUSTUS\tCDS\t5583\t5652\t0.26\t-\t0\ttranscript_id \"g1.t1\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t5592\t5594\tscaffold6_cov64\tAUGUSTUS\tCDS\t5583\t5652\t0.26\t-\t0\ttranscript_id \"g1.t1\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t5593\t5594\tscaffold6_cov64\tAUGUSTUS\tCDS\t5594\t5652\t0.54\t-\t0\ttranscript_id \"g1.t2\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t5594\t5596\tscaffold6_cov64\tAUGUSTUS\tCDS\t5583\t5652\t0.26\t-\t0\ttranscript_id \"g1.t1\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t5594\t5596\tscaffold6_cov64\tAUGUSTUS\tCDS\t5594\t5652\t0.54\t-\t0\ttranscript_id \"g1.t2\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t5604\t5606\tscaffold6_cov64\tAUGUSTUS\tCDS\t5583\t5652\t0.26\t-\t0\ttranscript_id \"g1.t1\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t5604\t5606\tscaffold6_cov64\tAUGUSTUS\tCDS\t5594\t5652\t0.54\t-\t0\ttranscript_id \"g1.t2\"; gene_id \"g1\";\r\n", "\r\n", "==> Meth9_R1_001_val_1_bismark_bt2_pe._10x.bedgraph.bed-paCDS <==\r\n", "scaffold6_cov64\t2179\t2181\tscaffold6_cov64\tAUGUSTUS\tCDS\t1922\t2269\t1\t-\t2\ttranscript_id \"g1.t1\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t2179\t2181\tscaffold6_cov64\tAUGUSTUS\tCDS\t1922\t2269\t1\t-\t2\ttranscript_id \"g1.t2\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t5582\t5583\tscaffold6_cov64\tAUGUSTUS\tCDS\t5583\t5652\t0.26\t-\t0\ttranscript_id \"g1.t1\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t5583\t5585\tscaffold6_cov64\tAUGUSTUS\tCDS\t5583\t5652\t0.26\t-\t0\ttranscript_id \"g1.t1\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t5592\t5594\tscaffold6_cov64\tAUGUSTUS\tCDS\t5583\t5652\t0.26\t-\t0\ttranscript_id \"g1.t1\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t5593\t5594\tscaffold6_cov64\tAUGUSTUS\tCDS\t5594\t5652\t0.54\t-\t0\ttranscript_id \"g1.t2\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t5594\t5596\tscaffold6_cov64\tAUGUSTUS\tCDS\t5583\t5652\t0.26\t-\t0\ttranscript_id \"g1.t1\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t5594\t5596\tscaffold6_cov64\tAUGUSTUS\tCDS\t5594\t5652\t0.54\t-\t0\ttranscript_id \"g1.t2\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t5604\t5606\tscaffold6_cov64\tAUGUSTUS\tCDS\t5583\t5652\t0.26\t-\t0\ttranscript_id \"g1.t1\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t5604\t5606\tscaffold6_cov64\tAUGUSTUS\tCDS\t5594\t5652\t0.54\t-\t0\ttranscript_id \"g1.t2\"; gene_id \"g1\";\r\n" ] } ], "source": [ "#Check output\n", "!head *paCDS" ] }, { "cell_type": "code", "execution_count": 107, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ " 23872 Meth1_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-Meth.bed-paCDS\n", " 26408 Meth1_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-sparseMeth.bed-paCDS\n", " 800209 Meth1_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-unMeth.bed-paCDS\n", " 850489 Meth1_R1_001_val_1_bismark_bt2_pe._10x.bedgraph.bed-paCDS\n", " 41839 Meth2_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-Meth.bed-paCDS\n", " 34947 Meth2_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-sparseMeth.bed-paCDS\n", " 1143040 Meth2_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-unMeth.bed-paCDS\n", " 1219826 Meth2_R1_001_val_1_bismark_bt2_pe._10x.bedgraph.bed-paCDS\n", " 32069 Meth3_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-Meth.bed-paCDS\n", " 32550 Meth3_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-sparseMeth.bed-paCDS\n", " 946018 Meth3_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-unMeth.bed-paCDS\n", " 1010637 Meth3_R1_001_val_1_bismark_bt2_pe._10x.bedgraph.bed-paCDS\n", " 3840 Meth4_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-Meth.bed-paCDS\n", " 18125 Meth4_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-sparseMeth.bed-paCDS\n", " 312874 Meth4_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-unMeth.bed-paCDS\n", " 334839 Meth4_R1_001_val_1_bismark_bt2_pe._10x.bedgraph.bed-paCDS\n", " 4217 Meth5_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-Meth.bed-paCDS\n", " 7617 Meth5_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-sparseMeth.bed-paCDS\n", " 263582 Meth5_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-unMeth.bed-paCDS\n", " 275416 Meth5_R1_001_val_1_bismark_bt2_pe._10x.bedgraph.bed-paCDS\n", " 3230 Meth6_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-Meth.bed-paCDS\n", " 10420 Meth6_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-sparseMeth.bed-paCDS\n", " 269605 Meth6_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-unMeth.bed-paCDS\n", " 283255 Meth6_R1_001_val_1_bismark_bt2_pe._10x.bedgraph.bed-paCDS\n", " 72744 Meth7_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-Meth.bed-paCDS\n", " 24809 Meth7_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-sparseMeth.bed-paCDS\n", " 187303 Meth7_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-unMeth.bed-paCDS\n", " 284856 Meth7_R1_001_val_1_bismark_bt2_pe._10x.bedgraph.bed-paCDS\n", " 51129 Meth8_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-Meth.bed-paCDS\n", " 9109 Meth8_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-sparseMeth.bed-paCDS\n", " 13002 Meth8_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-unMeth.bed-paCDS\n", " 73240 Meth8_R1_001_val_1_bismark_bt2_pe._10x.bedgraph.bed-paCDS\n", " 75705 Meth9_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-Meth.bed-paCDS\n", " 26175 Meth9_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-sparseMeth.bed-paCDS\n", " 163930 Meth9_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-unMeth.bed-paCDS\n", " 265810 Meth9_R1_001_val_1_bismark_bt2_pe._10x.bedgraph.bed-paCDS\n", " 9196736 total\n" ] } ], "source": [ "#Count number of overlaps\n", "!wc -l *paCDS" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "#### 4d. Introns" ] }, { "cell_type": "code", "execution_count": 108, "metadata": { "collapsed": true, "scrolled": true }, "outputs": [], "source": [ "%%bash\n", "\n", "for f in *bed\n", "do\n", " /usr/local/bin/intersectBed \\\n", " -wb \\\n", " -a ${f} \\\n", " -b ../../../genome-feature-files/Pact.GFFannotation.Intron.gff \\\n", " > ${f}-paIntron\n", "done" ] }, { "cell_type": "code", "execution_count": 109, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "==> Meth1_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-Meth.bed-paIntron <==\r\n", "scaffold7_cov100\t7438\t7440\tscaffold7_cov100\tAUGUSTUS\tintron\t7104\t7649\t1\t-\t.\ttranscript_id \"g5.t1\"; gene_id \"g5\";\r\n", "scaffold7_cov100\t7438\t7440\tscaffold7_cov100\tAUGUSTUS\tintron\t7104\t7649\t1\t-\t.\ttranscript_id \"g5.t2\"; gene_id \"g5\";\r\n", "scaffold7_cov100\t7891\t7892\tscaffold7_cov100\tAUGUSTUS\tintron\t7716\t7892\t1\t-\t.\ttranscript_id \"g5.t1\"; gene_id \"g5\";\r\n", "scaffold7_cov100\t7891\t7892\tscaffold7_cov100\tAUGUSTUS\tintron\t7716\t7892\t1\t-\t.\ttranscript_id \"g5.t2\"; gene_id \"g5\";\r\n", "scaffold7_cov100\t18941\t18943\tscaffold7_cov100\tAUGUSTUS\tintron\t18757\t19234\t0.99\t-\t.\ttranscript_id \"g9.t1\"; gene_id \"g9\";\r\n", "scaffold7_cov100\t21273\t21275\tscaffold7_cov100\tAUGUSTUS\tintron\t20697\t24051\t0.49\t+\t.\ttranscript_id \"g11.t1\"; gene_id \"g11\";\r\n", "scaffold7_cov100\t50493\t50495\tscaffold7_cov100\tAUGUSTUS\tintron\t50191\t50604\t1\t+\t.\ttranscript_id \"g16.t1\"; gene_id \"g16\";\r\n", "scaffold7_cov100\t69268\t69270\tscaffold7_cov100\tAUGUSTUS\tintron\t69212\t69346\t1\t-\t.\ttranscript_id \"g18.t1\"; gene_id \"g18\";\r\n", "scaffold7_cov100\t141310\t141312\tscaffold7_cov100\tAUGUSTUS\tintron\t140523\t141460\t1\t-\t.\ttranscript_id \"g35.t1\"; gene_id \"g35\";\r\n", "scaffold7_cov100\t250639\t250641\tscaffold7_cov100\tAUGUSTUS\tintron\t250529\t251080\t0.98\t+\t.\ttranscript_id \"g52.t1\"; gene_id \"g52\";\r\n", "\r\n", "==> Meth1_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-sparseMeth.bed-paIntron <==\r\n", "scaffold7_cov100\t4481\t4483\tscaffold7_cov100\tAUGUSTUS\tintron\t4181\t4607\t1\t-\t.\ttranscript_id \"g4.t1\"; gene_id \"g4\";\r\n", "scaffold7_cov100\t4481\t4483\tscaffold7_cov100\tAUGUSTUS\tintron\t4181\t4607\t1\t-\t.\ttranscript_id \"g4.t2\"; gene_id \"g4\";\r\n", "scaffold7_cov100\t4596\t4598\tscaffold7_cov100\tAUGUSTUS\tintron\t4181\t4607\t1\t-\t.\ttranscript_id \"g4.t1\"; gene_id \"g4\";\r\n", "scaffold7_cov100\t4596\t4598\tscaffold7_cov100\tAUGUSTUS\tintron\t4181\t4607\t1\t-\t.\ttranscript_id \"g4.t2\"; gene_id \"g4\";\r\n", "scaffold7_cov100\t55300\t55302\tscaffold7_cov100\tAUGUSTUS\tintron\t55069\t55438\t1\t+\t.\ttranscript_id \"g16.t1\"; gene_id \"g16\";\r\n", "scaffold7_cov100\t58794\t58796\tscaffold7_cov100\tAUGUSTUS\tintron\t58662\t59051\t1\t+\t.\ttranscript_id \"g16.t1\"; gene_id \"g16\";\r\n", "scaffold7_cov100\t96998\t97000\tscaffold7_cov100\tAUGUSTUS\tintron\t96870\t97263\t0.96\t-\t.\ttranscript_id \"g24.t1\"; gene_id \"g24\";\r\n", "scaffold7_cov100\t96998\t97000\tscaffold7_cov100\tAUGUSTUS\tintron\t96870\t97263\t0.96\t-\t.\ttranscript_id \"g24.t2\"; gene_id \"g24\";\r\n", "scaffold7_cov100\t97166\t97168\tscaffold7_cov100\tAUGUSTUS\tintron\t96870\t97263\t0.96\t-\t.\ttranscript_id \"g24.t1\"; gene_id \"g24\";\r\n", "scaffold7_cov100\t97166\t97168\tscaffold7_cov100\tAUGUSTUS\tintron\t96870\t97263\t0.96\t-\t.\ttranscript_id \"g24.t2\"; gene_id \"g24\";\r\n", "\r\n", "==> Meth1_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-unMeth.bed-paIntron <==\r\n", "scaffold6_cov64\t290\t292\tscaffold6_cov64\tAUGUSTUS\tintron\t1\t494\t0.82\t-\t.\ttranscript_id \"g1.t1\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t290\t292\tscaffold6_cov64\tAUGUSTUS\tintron\t1\t494\t0.82\t-\t.\ttranscript_id \"g1.t2\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t298\t300\tscaffold6_cov64\tAUGUSTUS\tintron\t1\t494\t0.82\t-\t.\ttranscript_id \"g1.t1\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t298\t300\tscaffold6_cov64\tAUGUSTUS\tintron\t1\t494\t0.82\t-\t.\ttranscript_id \"g1.t2\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t489\t491\tscaffold6_cov64\tAUGUSTUS\tintron\t1\t494\t0.82\t-\t.\ttranscript_id \"g1.t1\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t489\t491\tscaffold6_cov64\tAUGUSTUS\tintron\t1\t494\t0.82\t-\t.\ttranscript_id \"g1.t2\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t2805\t2807\tscaffold6_cov64\tAUGUSTUS\tintron\t2270\t5582\t0.23\t-\t.\ttranscript_id \"g1.t1\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t2805\t2807\tscaffold6_cov64\tAUGUSTUS\tintron\t2270\t4753\t0.4\t-\t.\ttranscript_id \"g1.t2\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t2876\t2878\tscaffold6_cov64\tAUGUSTUS\tintron\t2270\t5582\t0.23\t-\t.\ttranscript_id \"g1.t1\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t2876\t2878\tscaffold6_cov64\tAUGUSTUS\tintron\t2270\t4753\t0.4\t-\t.\ttranscript_id \"g1.t2\"; gene_id \"g1\";\r\n", "\r\n", "==> Meth1_R1_001_val_1_bismark_bt2_pe._10x.bedgraph.bed-paIntron <==\r\n", "scaffold6_cov64\t290\t292\tscaffold6_cov64\tAUGUSTUS\tintron\t1\t494\t0.82\t-\t.\ttranscript_id \"g1.t1\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t290\t292\tscaffold6_cov64\tAUGUSTUS\tintron\t1\t494\t0.82\t-\t.\ttranscript_id \"g1.t2\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t298\t300\tscaffold6_cov64\tAUGUSTUS\tintron\t1\t494\t0.82\t-\t.\ttranscript_id \"g1.t1\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t298\t300\tscaffold6_cov64\tAUGUSTUS\tintron\t1\t494\t0.82\t-\t.\ttranscript_id \"g1.t2\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t489\t491\tscaffold6_cov64\tAUGUSTUS\tintron\t1\t494\t0.82\t-\t.\ttranscript_id \"g1.t1\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t489\t491\tscaffold6_cov64\tAUGUSTUS\tintron\t1\t494\t0.82\t-\t.\ttranscript_id \"g1.t2\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t2805\t2807\tscaffold6_cov64\tAUGUSTUS\tintron\t2270\t5582\t0.23\t-\t.\ttranscript_id \"g1.t1\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t2805\t2807\tscaffold6_cov64\tAUGUSTUS\tintron\t2270\t4753\t0.4\t-\t.\ttranscript_id \"g1.t2\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t2876\t2878\tscaffold6_cov64\tAUGUSTUS\tintron\t2270\t5582\t0.23\t-\t.\ttranscript_id \"g1.t1\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t2876\t2878\tscaffold6_cov64\tAUGUSTUS\tintron\t2270\t4753\t0.4\t-\t.\ttranscript_id \"g1.t2\"; gene_id \"g1\";\r\n", "\r\n", "==> Meth2_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-Meth.bed-paIntron <==\r\n", "scaffold7_cov100\t7438\t7440\tscaffold7_cov100\tAUGUSTUS\tintron\t7104\t7649\t1\t-\t.\ttranscript_id \"g5.t1\"; gene_id \"g5\";\r\n", "scaffold7_cov100\t7438\t7440\tscaffold7_cov100\tAUGUSTUS\tintron\t7104\t7649\t1\t-\t.\ttranscript_id \"g5.t2\"; gene_id \"g5\";\r\n", "scaffold7_cov100\t7796\t7798\tscaffold7_cov100\tAUGUSTUS\tintron\t7716\t7892\t1\t-\t.\ttranscript_id \"g5.t1\"; gene_id \"g5\";\r\n", "scaffold7_cov100\t7796\t7798\tscaffold7_cov100\tAUGUSTUS\tintron\t7716\t7892\t1\t-\t.\ttranscript_id \"g5.t2\"; gene_id \"g5\";\r\n", "scaffold7_cov100\t7891\t7892\tscaffold7_cov100\tAUGUSTUS\tintron\t7716\t7892\t1\t-\t.\ttranscript_id \"g5.t1\"; gene_id \"g5\";\r\n", "scaffold7_cov100\t7891\t7892\tscaffold7_cov100\tAUGUSTUS\tintron\t7716\t7892\t1\t-\t.\ttranscript_id \"g5.t2\"; gene_id \"g5\";\r\n", "scaffold7_cov100\t10414\t10416\tscaffold7_cov100\tAUGUSTUS\tintron\t10282\t10594\t1\t-\t.\ttranscript_id \"g6.t1\"; gene_id \"g6\";\r\n", "scaffold7_cov100\t20228\t20230\tscaffold7_cov100\tAUGUSTUS\tintron\t20129\t20393\t0.8\t+\t.\ttranscript_id \"g11.t1\"; gene_id \"g11\";\r\n", "scaffold7_cov100\t20243\t20245\tscaffold7_cov100\tAUGUSTUS\tintron\t20129\t20393\t0.8\t+\t.\ttranscript_id \"g11.t1\"; gene_id \"g11\";\r\n", "scaffold7_cov100\t20259\t20261\tscaffold7_cov100\tAUGUSTUS\tintron\t20129\t20393\t0.8\t+\t.\ttranscript_id \"g11.t1\"; gene_id \"g11\";\r\n", "\r\n", "==> Meth2_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-sparseMeth.bed-paIntron <==\r\n", "scaffold6_cov64\t3978\t3980\tscaffold6_cov64\tAUGUSTUS\tintron\t2270\t5582\t0.23\t-\t.\ttranscript_id \"g1.t1\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t3978\t3980\tscaffold6_cov64\tAUGUSTUS\tintron\t2270\t4753\t0.4\t-\t.\ttranscript_id \"g1.t2\"; gene_id \"g1\";\r\n", "scaffold7_cov100\t3994\t3996\tscaffold7_cov100\tAUGUSTUS\tintron\t3590\t4057\t1\t-\t.\ttranscript_id \"g4.t1\"; gene_id \"g4\";\r\n", "scaffold7_cov100\t3994\t3996\tscaffold7_cov100\tAUGUSTUS\tintron\t3590\t4057\t1\t-\t.\ttranscript_id \"g4.t2\"; gene_id \"g4\";\r\n", "scaffold7_cov100\t7121\t7123\tscaffold7_cov100\tAUGUSTUS\tintron\t7104\t7649\t1\t-\t.\ttranscript_id \"g5.t1\"; gene_id \"g5\";\r\n", "scaffold7_cov100\t7121\t7123\tscaffold7_cov100\tAUGUSTUS\tintron\t7104\t7649\t1\t-\t.\ttranscript_id \"g5.t2\"; gene_id \"g5\";\r\n", "scaffold7_cov100\t7201\t7203\tscaffold7_cov100\tAUGUSTUS\tintron\t7104\t7649\t1\t-\t.\ttranscript_id \"g5.t1\"; gene_id \"g5\";\r\n", "scaffold7_cov100\t7201\t7203\tscaffold7_cov100\tAUGUSTUS\tintron\t7104\t7649\t1\t-\t.\ttranscript_id \"g5.t2\"; gene_id \"g5\";\r\n", "scaffold7_cov100\t11439\t11441\tscaffold7_cov100\tAUGUSTUS\tintron\t11392\t11471\t0.97\t-\t.\ttranscript_id \"g6.t1\"; gene_id \"g6\";\r\n", "scaffold7_cov100\t13385\t13387\tscaffold7_cov100\tAUGUSTUS\tintron\t13350\t13743\t0.99\t-\t.\ttranscript_id \"g7.t1\"; gene_id \"g7\";\r\n", "\r\n", "==> Meth2_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-unMeth.bed-paIntron <==\r\n", "scaffold6_cov64\t290\t292\tscaffold6_cov64\tAUGUSTUS\tintron\t1\t494\t0.82\t-\t.\ttranscript_id \"g1.t1\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t290\t292\tscaffold6_cov64\tAUGUSTUS\tintron\t1\t494\t0.82\t-\t.\ttranscript_id \"g1.t2\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t298\t300\tscaffold6_cov64\tAUGUSTUS\tintron\t1\t494\t0.82\t-\t.\ttranscript_id \"g1.t1\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t298\t300\tscaffold6_cov64\tAUGUSTUS\tintron\t1\t494\t0.82\t-\t.\ttranscript_id \"g1.t2\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t489\t491\tscaffold6_cov64\tAUGUSTUS\tintron\t1\t494\t0.82\t-\t.\ttranscript_id \"g1.t1\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t489\t491\tscaffold6_cov64\tAUGUSTUS\tintron\t1\t494\t0.82\t-\t.\ttranscript_id \"g1.t2\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t1725\t1727\tscaffold6_cov64\tAUGUSTUS\tintron\t1556\t1921\t1\t-\t.\ttranscript_id \"g1.t1\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t1725\t1727\tscaffold6_cov64\tAUGUSTUS\tintron\t1556\t1921\t1\t-\t.\ttranscript_id \"g1.t2\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t2676\t2678\tscaffold6_cov64\tAUGUSTUS\tintron\t2270\t5582\t0.23\t-\t.\ttranscript_id \"g1.t1\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t2676\t2678\tscaffold6_cov64\tAUGUSTUS\tintron\t2270\t4753\t0.4\t-\t.\ttranscript_id \"g1.t2\"; gene_id \"g1\";\r\n", "\r\n", "==> Meth2_R1_001_val_1_bismark_bt2_pe._10x.bedgraph.bed-paIntron <==\r\n", "scaffold6_cov64\t290\t292\tscaffold6_cov64\tAUGUSTUS\tintron\t1\t494\t0.82\t-\t.\ttranscript_id \"g1.t1\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t290\t292\tscaffold6_cov64\tAUGUSTUS\tintron\t1\t494\t0.82\t-\t.\ttranscript_id \"g1.t2\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t298\t300\tscaffold6_cov64\tAUGUSTUS\tintron\t1\t494\t0.82\t-\t.\ttranscript_id \"g1.t1\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t298\t300\tscaffold6_cov64\tAUGUSTUS\tintron\t1\t494\t0.82\t-\t.\ttranscript_id \"g1.t2\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t489\t491\tscaffold6_cov64\tAUGUSTUS\tintron\t1\t494\t0.82\t-\t.\ttranscript_id \"g1.t1\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t489\t491\tscaffold6_cov64\tAUGUSTUS\tintron\t1\t494\t0.82\t-\t.\ttranscript_id \"g1.t2\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t1725\t1727\tscaffold6_cov64\tAUGUSTUS\tintron\t1556\t1921\t1\t-\t.\ttranscript_id \"g1.t1\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t1725\t1727\tscaffold6_cov64\tAUGUSTUS\tintron\t1556\t1921\t1\t-\t.\ttranscript_id \"g1.t2\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t2676\t2678\tscaffold6_cov64\tAUGUSTUS\tintron\t2270\t5582\t0.23\t-\t.\ttranscript_id \"g1.t1\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t2676\t2678\tscaffold6_cov64\tAUGUSTUS\tintron\t2270\t4753\t0.4\t-\t.\ttranscript_id \"g1.t2\"; gene_id \"g1\";\r\n", "\r\n", "==> Meth3_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-Meth.bed-paIntron <==\r\n", "scaffold7_cov100\t7438\t7440\tscaffold7_cov100\tAUGUSTUS\tintron\t7104\t7649\t1\t-\t.\ttranscript_id \"g5.t1\"; gene_id \"g5\";\r\n", "scaffold7_cov100\t7438\t7440\tscaffold7_cov100\tAUGUSTUS\tintron\t7104\t7649\t1\t-\t.\ttranscript_id \"g5.t2\"; gene_id \"g5\";\r\n", "scaffold7_cov100\t7796\t7798\tscaffold7_cov100\tAUGUSTUS\tintron\t7716\t7892\t1\t-\t.\ttranscript_id \"g5.t1\"; gene_id \"g5\";\r\n", "scaffold7_cov100\t7796\t7798\tscaffold7_cov100\tAUGUSTUS\tintron\t7716\t7892\t1\t-\t.\ttranscript_id \"g5.t2\"; gene_id \"g5\";\r\n", "scaffold7_cov100\t13385\t13387\tscaffold7_cov100\tAUGUSTUS\tintron\t13350\t13743\t0.99\t-\t.\ttranscript_id \"g7.t1\"; gene_id \"g7\";\r\n", "scaffold7_cov100\t18941\t18943\tscaffold7_cov100\tAUGUSTUS\tintron\t18757\t19234\t0.99\t-\t.\ttranscript_id \"g9.t1\"; gene_id \"g9\";\r\n", "scaffold7_cov100\t21273\t21275\tscaffold7_cov100\tAUGUSTUS\tintron\t20697\t24051\t0.49\t+\t.\ttranscript_id \"g11.t1\"; gene_id \"g11\";\r\n", "scaffold7_cov100\t23298\t23300\tscaffold7_cov100\tAUGUSTUS\tintron\t20697\t24051\t0.49\t+\t.\ttranscript_id \"g11.t1\"; gene_id \"g11\";\r\n", "scaffold7_cov100\t50493\t50495\tscaffold7_cov100\tAUGUSTUS\tintron\t50191\t50604\t1\t+\t.\ttranscript_id \"g16.t1\"; gene_id \"g16\";\r\n", "scaffold7_cov100\t52058\t52060\tscaffold7_cov100\tAUGUSTUS\tintron\t51765\t52111\t1\t+\t.\ttranscript_id \"g16.t1\"; gene_id \"g16\";\r\n", "\r\n", "==> Meth3_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-sparseMeth.bed-paIntron <==\r\n", "scaffold7_cov100\t11439\t11441\tscaffold7_cov100\tAUGUSTUS\tintron\t11392\t11471\t0.97\t-\t.\ttranscript_id \"g6.t1\"; gene_id \"g6\";\r\n", "scaffold7_cov100\t13450\t13452\tscaffold7_cov100\tAUGUSTUS\tintron\t13350\t13743\t0.99\t-\t.\ttranscript_id \"g7.t1\"; gene_id \"g7\";\r\n", "scaffold7_cov100\t69313\t69315\tscaffold7_cov100\tAUGUSTUS\tintron\t69212\t69346\t1\t-\t.\ttranscript_id \"g18.t1\"; gene_id \"g18\";\r\n", "scaffold7_cov100\t75350\t75352\tscaffold7_cov100\tAUGUSTUS\tintron\t75267\t75419\t1\t-\t.\ttranscript_id \"g19.t1\"; gene_id \"g19\";\r\n", "scaffold7_cov100\t75955\t75957\tscaffold7_cov100\tAUGUSTUS\tintron\t75809\t76544\t1\t-\t.\ttranscript_id \"g19.t1\"; gene_id \"g19\";\r\n", "scaffold7_cov100\t96037\t96039\tscaffold7_cov100\tAUGUSTUS\tintron\t95895\t96067\t1\t-\t.\ttranscript_id \"g24.t1\"; gene_id \"g24\";\r\n", "scaffold7_cov100\t96037\t96039\tscaffold7_cov100\tAUGUSTUS\tintron\t95895\t96067\t1\t-\t.\ttranscript_id \"g24.t2\"; gene_id \"g24\";\r\n", "scaffold7_cov100\t98616\t98618\tscaffold7_cov100\tAUGUSTUS\tintron\t98271\t98881\t0.46\t-\t.\ttranscript_id \"g24.t2\"; gene_id \"g24\";\r\n", "scaffold7_cov100\t109687\t109689\tscaffold7_cov100\tAUGUSTUS\tintron\t109561\t110607\t0.74\t+\t.\ttranscript_id \"g28.t1\"; gene_id \"g28\";\r\n", "scaffold7_cov100\t109687\t109689\tscaffold7_cov100\tAUGUSTUS\tintron\t109561\t110607\t0.74\t+\t.\ttranscript_id \"g28.t2\"; gene_id \"g28\";\r\n", "\r\n", "==> Meth3_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-unMeth.bed-paIntron <==\r\n", "scaffold6_cov64\t290\t292\tscaffold6_cov64\tAUGUSTUS\tintron\t1\t494\t0.82\t-\t.\ttranscript_id \"g1.t1\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t290\t292\tscaffold6_cov64\tAUGUSTUS\tintron\t1\t494\t0.82\t-\t.\ttranscript_id \"g1.t2\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t298\t300\tscaffold6_cov64\tAUGUSTUS\tintron\t1\t494\t0.82\t-\t.\ttranscript_id \"g1.t1\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t298\t300\tscaffold6_cov64\tAUGUSTUS\tintron\t1\t494\t0.82\t-\t.\ttranscript_id \"g1.t2\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t489\t491\tscaffold6_cov64\tAUGUSTUS\tintron\t1\t494\t0.82\t-\t.\ttranscript_id \"g1.t1\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t489\t491\tscaffold6_cov64\tAUGUSTUS\tintron\t1\t494\t0.82\t-\t.\ttranscript_id \"g1.t2\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t2676\t2678\tscaffold6_cov64\tAUGUSTUS\tintron\t2270\t5582\t0.23\t-\t.\ttranscript_id \"g1.t1\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t2676\t2678\tscaffold6_cov64\tAUGUSTUS\tintron\t2270\t4753\t0.4\t-\t.\ttranscript_id \"g1.t2\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t2682\t2684\tscaffold6_cov64\tAUGUSTUS\tintron\t2270\t5582\t0.23\t-\t.\ttranscript_id \"g1.t1\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t2682\t2684\tscaffold6_cov64\tAUGUSTUS\tintron\t2270\t4753\t0.4\t-\t.\ttranscript_id \"g1.t2\"; gene_id \"g1\";\r\n", "\r\n", "==> Meth3_R1_001_val_1_bismark_bt2_pe._10x.bedgraph.bed-paIntron <==\r\n", "scaffold6_cov64\t290\t292\tscaffold6_cov64\tAUGUSTUS\tintron\t1\t494\t0.82\t-\t.\ttranscript_id \"g1.t1\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t290\t292\tscaffold6_cov64\tAUGUSTUS\tintron\t1\t494\t0.82\t-\t.\ttranscript_id \"g1.t2\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t298\t300\tscaffold6_cov64\tAUGUSTUS\tintron\t1\t494\t0.82\t-\t.\ttranscript_id \"g1.t1\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t298\t300\tscaffold6_cov64\tAUGUSTUS\tintron\t1\t494\t0.82\t-\t.\ttranscript_id \"g1.t2\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t489\t491\tscaffold6_cov64\tAUGUSTUS\tintron\t1\t494\t0.82\t-\t.\ttranscript_id \"g1.t1\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t489\t491\tscaffold6_cov64\tAUGUSTUS\tintron\t1\t494\t0.82\t-\t.\ttranscript_id \"g1.t2\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t2676\t2678\tscaffold6_cov64\tAUGUSTUS\tintron\t2270\t5582\t0.23\t-\t.\ttranscript_id \"g1.t1\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t2676\t2678\tscaffold6_cov64\tAUGUSTUS\tintron\t2270\t4753\t0.4\t-\t.\ttranscript_id \"g1.t2\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t2682\t2684\tscaffold6_cov64\tAUGUSTUS\tintron\t2270\t5582\t0.23\t-\t.\ttranscript_id \"g1.t1\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t2682\t2684\tscaffold6_cov64\tAUGUSTUS\tintron\t2270\t4753\t0.4\t-\t.\ttranscript_id \"g1.t2\"; gene_id \"g1\";\r\n", "\r\n", "==> Meth4_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-Meth.bed-paIntron <==\r\n", "scaffold7_cov100\t109716\t109718\tscaffold7_cov100\tAUGUSTUS\tintron\t109561\t110607\t0.74\t+\t.\ttranscript_id \"g28.t1\"; gene_id \"g28\";\r\n", "scaffold7_cov100\t109716\t109718\tscaffold7_cov100\tAUGUSTUS\tintron\t109561\t110607\t0.74\t+\t.\ttranscript_id \"g28.t2\"; gene_id \"g28\";\r\n", "scaffold7_cov100\t394699\t394701\tscaffold7_cov100\tAUGUSTUS\tintron\t392150\t394859\t0.56\t-\t.\ttranscript_id \"g86.t1\"; gene_id \"g86\";\r\n", "scaffold19_cov103\t93979\t93981\tscaffold19_cov103\tAUGUSTUS\tintron\t93636\t94251\t0.88\t-\t.\ttranscript_id \"g161.t1\"; gene_id \"g161\";\r\n", "scaffold19_cov103\t94067\t94069\tscaffold19_cov103\tAUGUSTUS\tintron\t93636\t94251\t0.88\t-\t.\ttranscript_id \"g161.t1\"; gene_id \"g161\";\r\n", "scaffold19_cov103\t94095\t94097\tscaffold19_cov103\tAUGUSTUS\tintron\t93636\t94251\t0.88\t-\t.\ttranscript_id \"g161.t1\"; gene_id \"g161\";\r\n", "scaffold19_cov103\t94119\t94121\tscaffold19_cov103\tAUGUSTUS\tintron\t93636\t94251\t0.88\t-\t.\ttranscript_id \"g161.t1\"; gene_id \"g161\";\r\n", "scaffold19_cov103\t94126\t94128\tscaffold19_cov103\tAUGUSTUS\tintron\t93636\t94251\t0.88\t-\t.\ttranscript_id \"g161.t1\"; gene_id \"g161\";\r\n", "scaffold19_cov103\t94135\t94137\tscaffold19_cov103\tAUGUSTUS\tintron\t93636\t94251\t0.88\t-\t.\ttranscript_id \"g161.t1\"; gene_id \"g161\";\r\n", "scaffold19_cov103\t121701\t121703\tscaffold19_cov103\tAUGUSTUS\tintron\t121611\t122621\t0.79\t+\t.\ttranscript_id \"g173.t1\"; gene_id \"g173\";\r\n", "\r\n", "==> Meth4_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-sparseMeth.bed-paIntron <==\r\n", "scaffold6_cov64\t5904\t5906\tscaffold6_cov64\tAUGUSTUS\tintron\t5839\t5945\t0.54\t+\t.\ttranscript_id \"g2.t1\"; gene_id \"g2\";\r\n", "scaffold6_cov64\t5904\t5906\tscaffold6_cov64\tAUGUSTUS\tintron\t5839\t5981\t0.44\t+\t.\ttranscript_id \"g2.t2\"; gene_id \"g2\";\r\n", "scaffold7_cov100\t4351\t4353\tscaffold7_cov100\tAUGUSTUS\tintron\t4181\t4607\t1\t-\t.\ttranscript_id \"g4.t1\"; gene_id \"g4\";\r\n", "scaffold7_cov100\t4351\t4353\tscaffold7_cov100\tAUGUSTUS\tintron\t4181\t4607\t1\t-\t.\ttranscript_id \"g4.t2\"; gene_id \"g4\";\r\n", "scaffold7_cov100\t81500\t81502\tscaffold7_cov100\tAUGUSTUS\tintron\t80878\t81739\t1\t-\t.\ttranscript_id \"g22.t1\"; gene_id \"g22\";\r\n", "scaffold7_cov100\t91941\t91942\tscaffold7_cov100\tAUGUSTUS\tintron\t91224\t91942\t0.72\t-\t.\ttranscript_id \"g23.t1\"; gene_id \"g23\";\r\n", "scaffold7_cov100\t177838\t177840\tscaffold7_cov100\tAUGUSTUS\tintron\t177336\t177959\t1\t-\t.\ttranscript_id \"g44.t1\"; gene_id \"g44\";\r\n", "scaffold7_cov100\t177838\t177840\tscaffold7_cov100\tAUGUSTUS\tintron\t177336\t177959\t1\t-\t.\ttranscript_id \"g44.t2\"; gene_id \"g44\";\r\n", "scaffold7_cov100\t181717\t181719\tscaffold7_cov100\tAUGUSTUS\tintron\t181500\t181847\t1\t-\t.\ttranscript_id \"g44.t1\"; gene_id \"g44\";\r\n", "scaffold7_cov100\t181717\t181719\tscaffold7_cov100\tAUGUSTUS\tintron\t181500\t181847\t1\t-\t.\ttranscript_id \"g44.t2\"; gene_id \"g44\";\r\n", "\r\n", "==> Meth4_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-unMeth.bed-paIntron <==\r\n", "scaffold6_cov64\t5456\t5458\tscaffold6_cov64\tAUGUSTUS\tintron\t2270\t5582\t0.23\t-\t.\ttranscript_id \"g1.t1\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t5456\t5458\tscaffold6_cov64\tAUGUSTUS\tintron\t4852\t5593\t0.48\t-\t.\ttranscript_id \"g1.t2\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t5486\t5488\tscaffold6_cov64\tAUGUSTUS\tintron\t2270\t5582\t0.23\t-\t.\ttranscript_id \"g1.t1\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t5486\t5488\tscaffold6_cov64\tAUGUSTUS\tintron\t4852\t5593\t0.48\t-\t.\ttranscript_id \"g1.t2\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t5545\t5547\tscaffold6_cov64\tAUGUSTUS\tintron\t2270\t5582\t0.23\t-\t.\ttranscript_id \"g1.t1\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t5545\t5547\tscaffold6_cov64\tAUGUSTUS\tintron\t4852\t5593\t0.48\t-\t.\ttranscript_id \"g1.t2\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t5559\t5561\tscaffold6_cov64\tAUGUSTUS\tintron\t2270\t5582\t0.23\t-\t.\ttranscript_id \"g1.t1\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t5559\t5561\tscaffold6_cov64\tAUGUSTUS\tintron\t4852\t5593\t0.48\t-\t.\ttranscript_id \"g1.t2\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t5561\t5563\tscaffold6_cov64\tAUGUSTUS\tintron\t2270\t5582\t0.23\t-\t.\ttranscript_id \"g1.t1\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t5561\t5563\tscaffold6_cov64\tAUGUSTUS\tintron\t4852\t5593\t0.48\t-\t.\ttranscript_id \"g1.t2\"; gene_id \"g1\";\r\n", "\r\n", "==> Meth4_R1_001_val_1_bismark_bt2_pe._10x.bedgraph.bed-paIntron <==\r\n", "scaffold6_cov64\t5456\t5458\tscaffold6_cov64\tAUGUSTUS\tintron\t2270\t5582\t0.23\t-\t.\ttranscript_id \"g1.t1\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t5456\t5458\tscaffold6_cov64\tAUGUSTUS\tintron\t4852\t5593\t0.48\t-\t.\ttranscript_id \"g1.t2\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t5486\t5488\tscaffold6_cov64\tAUGUSTUS\tintron\t2270\t5582\t0.23\t-\t.\ttranscript_id \"g1.t1\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t5486\t5488\tscaffold6_cov64\tAUGUSTUS\tintron\t4852\t5593\t0.48\t-\t.\ttranscript_id \"g1.t2\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t5545\t5547\tscaffold6_cov64\tAUGUSTUS\tintron\t2270\t5582\t0.23\t-\t.\ttranscript_id \"g1.t1\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t5545\t5547\tscaffold6_cov64\tAUGUSTUS\tintron\t4852\t5593\t0.48\t-\t.\ttranscript_id \"g1.t2\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t5559\t5561\tscaffold6_cov64\tAUGUSTUS\tintron\t2270\t5582\t0.23\t-\t.\ttranscript_id \"g1.t1\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t5559\t5561\tscaffold6_cov64\tAUGUSTUS\tintron\t4852\t5593\t0.48\t-\t.\ttranscript_id \"g1.t2\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t5561\t5563\tscaffold6_cov64\tAUGUSTUS\tintron\t2270\t5582\t0.23\t-\t.\ttranscript_id \"g1.t1\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t5561\t5563\tscaffold6_cov64\tAUGUSTUS\tintron\t4852\t5593\t0.48\t-\t.\ttranscript_id \"g1.t2\"; gene_id \"g1\";\r\n", "\r\n", "==> Meth5_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-Meth.bed-paIntron <==\r\n", "scaffold7_cov100\t177834\t177836\tscaffold7_cov100\tAUGUSTUS\tintron\t177336\t177959\t1\t-\t.\ttranscript_id \"g44.t1\"; gene_id \"g44\";\r\n", "scaffold7_cov100\t177834\t177836\tscaffold7_cov100\tAUGUSTUS\tintron\t177336\t177959\t1\t-\t.\ttranscript_id \"g44.t2\"; gene_id \"g44\";\r\n", "scaffold7_cov100\t177838\t177840\tscaffold7_cov100\tAUGUSTUS\tintron\t177336\t177959\t1\t-\t.\ttranscript_id \"g44.t1\"; gene_id \"g44\";\r\n", "scaffold7_cov100\t177838\t177840\tscaffold7_cov100\tAUGUSTUS\tintron\t177336\t177959\t1\t-\t.\ttranscript_id \"g44.t2\"; gene_id \"g44\";\r\n", "scaffold7_cov100\t253591\t253593\tscaffold7_cov100\tAUGUSTUS\tintron\t253354\t253848\t0.97\t-\t.\ttranscript_id \"g53.t1\"; gene_id \"g53\";\r\n", "scaffold7_cov100\t394699\t394701\tscaffold7_cov100\tAUGUSTUS\tintron\t392150\t394859\t0.56\t-\t.\ttranscript_id \"g86.t1\"; gene_id \"g86\";\r\n", "scaffold19_cov103\t187941\t187943\tscaffold19_cov103\tAUGUSTUS\tintron\t187855\t188113\t1\t-\t.\ttranscript_id \"g189.t1\"; gene_id \"g189\";\r\n", "scaffold20_cov103\t58143\t58145\tscaffold20_cov103\tAUGUSTUS\tintron\t57952\t58402\t1\t-\t.\ttranscript_id \"g215.t1\"; gene_id \"g215\";\r\n", "scaffold27_cov99\t96395\t96397\tscaffold27_cov99\tAUGUSTUS\tintron\t96151\t97133\t1\t-\t.\ttranscript_id \"g259.t1\"; gene_id \"g259\";\r\n", "scaffold27_cov99\t96395\t96397\tscaffold27_cov99\tAUGUSTUS\tintron\t96151\t97133\t1\t-\t.\ttranscript_id \"g259.t2\"; gene_id \"g259\";\r\n", "\r\n", "==> Meth5_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-sparseMeth.bed-paIntron <==\r\n", "scaffold6_cov64\t6374\t6376\tscaffold6_cov64\tAUGUSTUS\tintron\t6268\t6566\t0.58\t+\t.\ttranscript_id \"g2.t1\"; gene_id \"g2\";\r\n", "scaffold6_cov64\t6374\t6376\tscaffold6_cov64\tAUGUSTUS\tintron\t6268\t6566\t0.58\t+\t.\ttranscript_id \"g2.t2\"; gene_id \"g2\";\r\n", "scaffold7_cov100\t177836\t177838\tscaffold7_cov100\tAUGUSTUS\tintron\t177336\t177959\t1\t-\t.\ttranscript_id \"g44.t1\"; gene_id \"g44\";\r\n", "scaffold7_cov100\t177836\t177838\tscaffold7_cov100\tAUGUSTUS\tintron\t177336\t177959\t1\t-\t.\ttranscript_id \"g44.t2\"; gene_id \"g44\";\r\n", "scaffold7_cov100\t404820\t404822\tscaffold7_cov100\tAUGUSTUS\tintron\t404713\t405138\t0.35\t+\t.\ttranscript_id \"g87.t2\"; gene_id \"g87\";\r\n", "scaffold7_cov100\t494482\t494484\tscaffold7_cov100\tAUGUSTUS\tintron\t493431\t495191\t1\t+\t.\ttranscript_id \"g110.t1\"; gene_id \"g110\";\r\n", "scaffold7_cov100\t494511\t494513\tscaffold7_cov100\tAUGUSTUS\tintron\t493431\t495191\t1\t+\t.\ttranscript_id \"g110.t1\"; gene_id \"g110\";\r\n", "scaffold7_cov100\t494547\t494549\tscaffold7_cov100\tAUGUSTUS\tintron\t493431\t495191\t1\t+\t.\ttranscript_id \"g110.t1\"; gene_id \"g110\";\r\n", "scaffold7_cov100\t494553\t494555\tscaffold7_cov100\tAUGUSTUS\tintron\t493431\t495191\t1\t+\t.\ttranscript_id \"g110.t1\"; gene_id \"g110\";\r\n", "scaffold12_cov67\t4363\t4365\tscaffold12_cov67\tAUGUSTUS\tintron\t2824\t5159\t0.24\t+\t.\ttranscript_id \"g124.t1\"; gene_id \"g124\";\r\n", "\r\n", "==> Meth5_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-unMeth.bed-paIntron <==\r\n", "scaffold6_cov64\t4588\t4590\tscaffold6_cov64\tAUGUSTUS\tintron\t2270\t5582\t0.23\t-\t.\ttranscript_id \"g1.t1\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t4588\t4590\tscaffold6_cov64\tAUGUSTUS\tintron\t2270\t4753\t0.4\t-\t.\ttranscript_id \"g1.t2\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t5559\t5561\tscaffold6_cov64\tAUGUSTUS\tintron\t2270\t5582\t0.23\t-\t.\ttranscript_id \"g1.t1\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t5559\t5561\tscaffold6_cov64\tAUGUSTUS\tintron\t4852\t5593\t0.48\t-\t.\ttranscript_id \"g1.t2\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t5561\t5563\tscaffold6_cov64\tAUGUSTUS\tintron\t2270\t5582\t0.23\t-\t.\ttranscript_id \"g1.t1\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t5561\t5563\tscaffold6_cov64\tAUGUSTUS\tintron\t4852\t5593\t0.48\t-\t.\ttranscript_id \"g1.t2\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t5567\t5569\tscaffold6_cov64\tAUGUSTUS\tintron\t2270\t5582\t0.23\t-\t.\ttranscript_id \"g1.t1\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t5567\t5569\tscaffold6_cov64\tAUGUSTUS\tintron\t4852\t5593\t0.48\t-\t.\ttranscript_id \"g1.t2\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t5574\t5576\tscaffold6_cov64\tAUGUSTUS\tintron\t2270\t5582\t0.23\t-\t.\ttranscript_id \"g1.t1\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t5574\t5576\tscaffold6_cov64\tAUGUSTUS\tintron\t4852\t5593\t0.48\t-\t.\ttranscript_id \"g1.t2\"; gene_id \"g1\";\r\n", "\r\n", "==> Meth5_R1_001_val_1_bismark_bt2_pe._10x.bedgraph.bed-paIntron <==\r\n", "scaffold6_cov64\t4588\t4590\tscaffold6_cov64\tAUGUSTUS\tintron\t2270\t5582\t0.23\t-\t.\ttranscript_id \"g1.t1\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t4588\t4590\tscaffold6_cov64\tAUGUSTUS\tintron\t2270\t4753\t0.4\t-\t.\ttranscript_id \"g1.t2\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t5559\t5561\tscaffold6_cov64\tAUGUSTUS\tintron\t2270\t5582\t0.23\t-\t.\ttranscript_id \"g1.t1\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t5559\t5561\tscaffold6_cov64\tAUGUSTUS\tintron\t4852\t5593\t0.48\t-\t.\ttranscript_id \"g1.t2\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t5561\t5563\tscaffold6_cov64\tAUGUSTUS\tintron\t2270\t5582\t0.23\t-\t.\ttranscript_id \"g1.t1\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t5561\t5563\tscaffold6_cov64\tAUGUSTUS\tintron\t4852\t5593\t0.48\t-\t.\ttranscript_id \"g1.t2\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t5567\t5569\tscaffold6_cov64\tAUGUSTUS\tintron\t2270\t5582\t0.23\t-\t.\ttranscript_id \"g1.t1\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t5567\t5569\tscaffold6_cov64\tAUGUSTUS\tintron\t4852\t5593\t0.48\t-\t.\ttranscript_id \"g1.t2\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t5574\t5576\tscaffold6_cov64\tAUGUSTUS\tintron\t2270\t5582\t0.23\t-\t.\ttranscript_id \"g1.t1\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t5574\t5576\tscaffold6_cov64\tAUGUSTUS\tintron\t4852\t5593\t0.48\t-\t.\ttranscript_id \"g1.t2\"; gene_id \"g1\";\r\n", "\r\n", "==> Meth6_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-Meth.bed-paIntron <==\r\n", "scaffold7_cov100\t394699\t394701\tscaffold7_cov100\tAUGUSTUS\tintron\t392150\t394859\t0.56\t-\t.\ttranscript_id \"g86.t1\"; gene_id \"g86\";\r\n", "scaffold12_cov67\t4517\t4519\tscaffold12_cov67\tAUGUSTUS\tintron\t2824\t5159\t0.24\t+\t.\ttranscript_id \"g124.t1\"; gene_id \"g124\";\r\n", "scaffold12_cov67\t4517\t4519\tscaffold12_cov67\tAUGUSTUS\tintron\t4393\t5159\t0.25\t+\t.\ttranscript_id \"g124.t2\"; gene_id \"g124\";\r\n", "scaffold12_cov67\t11660\t11662\tscaffold12_cov67\tAUGUSTUS\tintron\t11633\t12241\t1\t+\t.\ttranscript_id \"g126.t1\"; gene_id \"g126\";\r\n", "scaffold19_cov103\t69462\t69464\tscaffold19_cov103\tAUGUSTUS\tintron\t69118\t69564\t1\t+\t.\ttranscript_id \"g155.t1\"; gene_id \"g155\";\r\n", "scaffold27_cov99\t17698\t17700\tscaffold27_cov99\tAUGUSTUS\tintron\t16490\t17886\t0.45\t-\t.\ttranscript_id \"g243.t1\"; gene_id \"g243\";\r\n", "scaffold28_cov97\t97312\t97314\tscaffold28_cov97\tAUGUSTUS\tintron\t97028\t97637\t1\t-\t.\ttranscript_id \"g291.t1\"; gene_id \"g291\";\r\n", "scaffold28_cov97\t106257\t106259\tscaffold28_cov97\tAUGUSTUS\tintron\t106117\t106376\t1\t-\t.\ttranscript_id \"g292.t1\"; gene_id \"g292\";\r\n", "scaffold28_cov97\t116011\t116013\tscaffold28_cov97\tAUGUSTUS\tintron\t115569\t116421\t0.54\t+\t.\ttranscript_id \"g293.t1\"; gene_id \"g293\";\r\n", "scaffold42_cov106\t194026\t194028\tscaffold42_cov106\tAUGUSTUS\tintron\t192906\t194382\t0.24\t-\t.\ttranscript_id \"g399.t1\"; gene_id \"g399\";\r\n", "\r\n", "==> Meth6_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-sparseMeth.bed-paIntron <==\r\n", "scaffold6_cov64\t6267\t6268\tscaffold6_cov64\tAUGUSTUS\tintron\t6268\t6566\t0.58\t+\t.\ttranscript_id \"g2.t1\"; gene_id \"g2\";\r\n", "scaffold6_cov64\t6267\t6268\tscaffold6_cov64\tAUGUSTUS\tintron\t6268\t6566\t0.58\t+\t.\ttranscript_id \"g2.t2\"; gene_id \"g2\";\r\n", "scaffold7_cov100\t4351\t4353\tscaffold7_cov100\tAUGUSTUS\tintron\t4181\t4607\t1\t-\t.\ttranscript_id \"g4.t1\"; gene_id \"g4\";\r\n", "scaffold7_cov100\t4351\t4353\tscaffold7_cov100\tAUGUSTUS\tintron\t4181\t4607\t1\t-\t.\ttranscript_id \"g4.t2\"; gene_id \"g4\";\r\n", "scaffold7_cov100\t32521\t32523\tscaffold7_cov100\tAUGUSTUS\tintron\t32002\t32891\t0.64\t-\t.\ttranscript_id \"g13.t1\"; gene_id \"g13\";\r\n", "scaffold7_cov100\t32521\t32523\tscaffold7_cov100\tAUGUSTUS\tintron\t32002\t32891\t0.64\t-\t.\ttranscript_id \"g13.t2\"; gene_id \"g13\";\r\n", "scaffold7_cov100\t82753\t82755\tscaffold7_cov100\tAUGUSTUS\tintron\t81869\t82759\t1\t-\t.\ttranscript_id \"g22.t1\"; gene_id \"g22\";\r\n", "scaffold7_cov100\t109704\t109706\tscaffold7_cov100\tAUGUSTUS\tintron\t109561\t110607\t0.74\t+\t.\ttranscript_id \"g28.t1\"; gene_id \"g28\";\r\n", "scaffold7_cov100\t109704\t109706\tscaffold7_cov100\tAUGUSTUS\tintron\t109561\t110607\t0.74\t+\t.\ttranscript_id \"g28.t2\"; gene_id \"g28\";\r\n", "scaffold7_cov100\t109716\t109718\tscaffold7_cov100\tAUGUSTUS\tintron\t109561\t110607\t0.74\t+\t.\ttranscript_id \"g28.t1\"; gene_id \"g28\";\r\n", "\r\n", "==> Meth6_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-unMeth.bed-paIntron <==\r\n", "scaffold6_cov64\t5545\t5547\tscaffold6_cov64\tAUGUSTUS\tintron\t2270\t5582\t0.23\t-\t.\ttranscript_id \"g1.t1\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t5545\t5547\tscaffold6_cov64\tAUGUSTUS\tintron\t4852\t5593\t0.48\t-\t.\ttranscript_id \"g1.t2\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t5559\t5561\tscaffold6_cov64\tAUGUSTUS\tintron\t2270\t5582\t0.23\t-\t.\ttranscript_id \"g1.t1\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t5559\t5561\tscaffold6_cov64\tAUGUSTUS\tintron\t4852\t5593\t0.48\t-\t.\ttranscript_id \"g1.t2\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t5561\t5563\tscaffold6_cov64\tAUGUSTUS\tintron\t2270\t5582\t0.23\t-\t.\ttranscript_id \"g1.t1\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t5561\t5563\tscaffold6_cov64\tAUGUSTUS\tintron\t4852\t5593\t0.48\t-\t.\ttranscript_id \"g1.t2\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t5567\t5569\tscaffold6_cov64\tAUGUSTUS\tintron\t2270\t5582\t0.23\t-\t.\ttranscript_id \"g1.t1\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t5567\t5569\tscaffold6_cov64\tAUGUSTUS\tintron\t4852\t5593\t0.48\t-\t.\ttranscript_id \"g1.t2\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t5574\t5576\tscaffold6_cov64\tAUGUSTUS\tintron\t2270\t5582\t0.23\t-\t.\ttranscript_id \"g1.t1\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t5574\t5576\tscaffold6_cov64\tAUGUSTUS\tintron\t4852\t5593\t0.48\t-\t.\ttranscript_id \"g1.t2\"; gene_id \"g1\";\r\n", "\r\n", "==> Meth6_R1_001_val_1_bismark_bt2_pe._10x.bedgraph.bed-paIntron <==\r\n", "scaffold6_cov64\t5545\t5547\tscaffold6_cov64\tAUGUSTUS\tintron\t2270\t5582\t0.23\t-\t.\ttranscript_id \"g1.t1\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t5545\t5547\tscaffold6_cov64\tAUGUSTUS\tintron\t4852\t5593\t0.48\t-\t.\ttranscript_id \"g1.t2\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t5559\t5561\tscaffold6_cov64\tAUGUSTUS\tintron\t2270\t5582\t0.23\t-\t.\ttranscript_id \"g1.t1\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t5559\t5561\tscaffold6_cov64\tAUGUSTUS\tintron\t4852\t5593\t0.48\t-\t.\ttranscript_id \"g1.t2\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t5561\t5563\tscaffold6_cov64\tAUGUSTUS\tintron\t2270\t5582\t0.23\t-\t.\ttranscript_id \"g1.t1\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t5561\t5563\tscaffold6_cov64\tAUGUSTUS\tintron\t4852\t5593\t0.48\t-\t.\ttranscript_id \"g1.t2\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t5567\t5569\tscaffold6_cov64\tAUGUSTUS\tintron\t2270\t5582\t0.23\t-\t.\ttranscript_id \"g1.t1\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t5567\t5569\tscaffold6_cov64\tAUGUSTUS\tintron\t4852\t5593\t0.48\t-\t.\ttranscript_id \"g1.t2\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t5574\t5576\tscaffold6_cov64\tAUGUSTUS\tintron\t2270\t5582\t0.23\t-\t.\ttranscript_id \"g1.t1\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t5574\t5576\tscaffold6_cov64\tAUGUSTUS\tintron\t4852\t5593\t0.48\t-\t.\ttranscript_id \"g1.t2\"; gene_id \"g1\";\r\n", "\r\n", "==> Meth7_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-Meth.bed-paIntron <==\r\n", "scaffold7_cov100\t5986\t5988\tscaffold7_cov100\tAUGUSTUS\tintron\t5541\t6090\t1\t-\t.\ttranscript_id \"g4.t1\"; gene_id \"g4\";\r\n", "scaffold7_cov100\t5986\t5988\tscaffold7_cov100\tAUGUSTUS\tintron\t5541\t6090\t1\t-\t.\ttranscript_id \"g4.t2\"; gene_id \"g4\";\r\n", "scaffold7_cov100\t7438\t7440\tscaffold7_cov100\tAUGUSTUS\tintron\t7104\t7649\t1\t-\t.\ttranscript_id \"g5.t1\"; gene_id \"g5\";\r\n", "scaffold7_cov100\t7438\t7440\tscaffold7_cov100\tAUGUSTUS\tintron\t7104\t7649\t1\t-\t.\ttranscript_id \"g5.t2\"; gene_id \"g5\";\r\n", "scaffold7_cov100\t7796\t7798\tscaffold7_cov100\tAUGUSTUS\tintron\t7716\t7892\t1\t-\t.\ttranscript_id \"g5.t1\"; gene_id \"g5\";\r\n", "scaffold7_cov100\t7796\t7798\tscaffold7_cov100\tAUGUSTUS\tintron\t7716\t7892\t1\t-\t.\ttranscript_id \"g5.t2\"; gene_id \"g5\";\r\n", "scaffold7_cov100\t7891\t7892\tscaffold7_cov100\tAUGUSTUS\tintron\t7716\t7892\t1\t-\t.\ttranscript_id \"g5.t1\"; gene_id \"g5\";\r\n", "scaffold7_cov100\t7891\t7892\tscaffold7_cov100\tAUGUSTUS\tintron\t7716\t7892\t1\t-\t.\ttranscript_id \"g5.t2\"; gene_id \"g5\";\r\n", "scaffold7_cov100\t10414\t10416\tscaffold7_cov100\tAUGUSTUS\tintron\t10282\t10594\t1\t-\t.\ttranscript_id \"g6.t1\"; gene_id \"g6\";\r\n", "scaffold7_cov100\t13385\t13387\tscaffold7_cov100\tAUGUSTUS\tintron\t13350\t13743\t0.99\t-\t.\ttranscript_id \"g7.t1\"; gene_id \"g7\";\r\n", "\r\n", "==> Meth7_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-sparseMeth.bed-paIntron <==\r\n", "scaffold7_cov100\t11439\t11441\tscaffold7_cov100\tAUGUSTUS\tintron\t11392\t11471\t0.97\t-\t.\ttranscript_id \"g6.t1\"; gene_id \"g6\";\r\n", "scaffold7_cov100\t52903\t52905\tscaffold7_cov100\tAUGUSTUS\tintron\t52812\t53071\t1\t+\t.\ttranscript_id \"g16.t1\"; gene_id \"g16\";\r\n", "scaffold7_cov100\t69313\t69315\tscaffold7_cov100\tAUGUSTUS\tintron\t69212\t69346\t1\t-\t.\ttranscript_id \"g18.t1\"; gene_id \"g18\";\r\n", "scaffold7_cov100\t89847\t89849\tscaffold7_cov100\tAUGUSTUS\tintron\t89767\t89903\t0.85\t-\t.\ttranscript_id \"g23.t1\"; gene_id \"g23\";\r\n", "scaffold7_cov100\t403487\t403489\tscaffold7_cov100\tAUGUSTUS\tintron\t403479\t403651\t1\t+\t.\ttranscript_id \"g87.t1\"; gene_id \"g87\";\r\n", "scaffold7_cov100\t403487\t403489\tscaffold7_cov100\tAUGUSTUS\tintron\t403479\t403651\t1\t+\t.\ttranscript_id \"g87.t2\"; gene_id \"g87\";\r\n", "scaffold7_cov100\t404747\t404749\tscaffold7_cov100\tAUGUSTUS\tintron\t404713\t405138\t0.35\t+\t.\ttranscript_id \"g87.t2\"; gene_id \"g87\";\r\n", "scaffold7_cov100\t439176\t439178\tscaffold7_cov100\tAUGUSTUS\tintron\t439060\t440240\t0.89\t-\t.\ttranscript_id \"g94.t1\"; gene_id \"g94\";\r\n", "scaffold7_cov100\t439205\t439207\tscaffold7_cov100\tAUGUSTUS\tintron\t439060\t440240\t0.89\t-\t.\ttranscript_id \"g94.t1\"; gene_id \"g94\";\r\n", "scaffold7_cov100\t449357\t449359\tscaffold7_cov100\tAUGUSTUS\tintron\t448944\t449410\t1\t+\t.\ttranscript_id \"g96.t1\"; gene_id \"g96\";\r\n", "\r\n", "==> Meth7_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-unMeth.bed-paIntron <==\r\n", "scaffold6_cov64\t489\t491\tscaffold6_cov64\tAUGUSTUS\tintron\t1\t494\t0.82\t-\t.\ttranscript_id \"g1.t1\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t489\t491\tscaffold6_cov64\tAUGUSTUS\tintron\t1\t494\t0.82\t-\t.\ttranscript_id \"g1.t2\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t3343\t3345\tscaffold6_cov64\tAUGUSTUS\tintron\t2270\t5582\t0.23\t-\t.\ttranscript_id \"g1.t1\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t3343\t3345\tscaffold6_cov64\tAUGUSTUS\tintron\t2270\t4753\t0.4\t-\t.\ttranscript_id \"g1.t2\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t3420\t3422\tscaffold6_cov64\tAUGUSTUS\tintron\t2270\t5582\t0.23\t-\t.\ttranscript_id \"g1.t1\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t3420\t3422\tscaffold6_cov64\tAUGUSTUS\tintron\t2270\t4753\t0.4\t-\t.\ttranscript_id \"g1.t2\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t3435\t3437\tscaffold6_cov64\tAUGUSTUS\tintron\t2270\t5582\t0.23\t-\t.\ttranscript_id \"g1.t1\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t3435\t3437\tscaffold6_cov64\tAUGUSTUS\tintron\t2270\t4753\t0.4\t-\t.\ttranscript_id \"g1.t2\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t3439\t3441\tscaffold6_cov64\tAUGUSTUS\tintron\t2270\t5582\t0.23\t-\t.\ttranscript_id \"g1.t1\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t3439\t3441\tscaffold6_cov64\tAUGUSTUS\tintron\t2270\t4753\t0.4\t-\t.\ttranscript_id \"g1.t2\"; gene_id \"g1\";\r\n", "\r\n", "==> Meth7_R1_001_val_1_bismark_bt2_pe._10x.bedgraph.bed-paIntron <==\r\n", "scaffold6_cov64\t489\t491\tscaffold6_cov64\tAUGUSTUS\tintron\t1\t494\t0.82\t-\t.\ttranscript_id \"g1.t1\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t489\t491\tscaffold6_cov64\tAUGUSTUS\tintron\t1\t494\t0.82\t-\t.\ttranscript_id \"g1.t2\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t3343\t3345\tscaffold6_cov64\tAUGUSTUS\tintron\t2270\t5582\t0.23\t-\t.\ttranscript_id \"g1.t1\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t3343\t3345\tscaffold6_cov64\tAUGUSTUS\tintron\t2270\t4753\t0.4\t-\t.\ttranscript_id \"g1.t2\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t3420\t3422\tscaffold6_cov64\tAUGUSTUS\tintron\t2270\t5582\t0.23\t-\t.\ttranscript_id \"g1.t1\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t3420\t3422\tscaffold6_cov64\tAUGUSTUS\tintron\t2270\t4753\t0.4\t-\t.\ttranscript_id \"g1.t2\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t3435\t3437\tscaffold6_cov64\tAUGUSTUS\tintron\t2270\t5582\t0.23\t-\t.\ttranscript_id \"g1.t1\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t3435\t3437\tscaffold6_cov64\tAUGUSTUS\tintron\t2270\t4753\t0.4\t-\t.\ttranscript_id \"g1.t2\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t3439\t3441\tscaffold6_cov64\tAUGUSTUS\tintron\t2270\t5582\t0.23\t-\t.\ttranscript_id \"g1.t1\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t3439\t3441\tscaffold6_cov64\tAUGUSTUS\tintron\t2270\t4753\t0.4\t-\t.\ttranscript_id \"g1.t2\"; gene_id \"g1\";\r\n", "\r\n", "==> Meth8_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-Meth.bed-paIntron <==\r\n", "scaffold7_cov100\t5986\t5988\tscaffold7_cov100\tAUGUSTUS\tintron\t5541\t6090\t1\t-\t.\ttranscript_id \"g4.t1\"; gene_id \"g4\";\r\n", "scaffold7_cov100\t5986\t5988\tscaffold7_cov100\tAUGUSTUS\tintron\t5541\t6090\t1\t-\t.\ttranscript_id \"g4.t2\"; gene_id \"g4\";\r\n", "scaffold7_cov100\t7796\t7798\tscaffold7_cov100\tAUGUSTUS\tintron\t7716\t7892\t1\t-\t.\ttranscript_id \"g5.t1\"; gene_id \"g5\";\r\n", "scaffold7_cov100\t7796\t7798\tscaffold7_cov100\tAUGUSTUS\tintron\t7716\t7892\t1\t-\t.\ttranscript_id \"g5.t2\"; gene_id \"g5\";\r\n", "scaffold7_cov100\t7891\t7892\tscaffold7_cov100\tAUGUSTUS\tintron\t7716\t7892\t1\t-\t.\ttranscript_id \"g5.t1\"; gene_id \"g5\";\r\n", "scaffold7_cov100\t7891\t7892\tscaffold7_cov100\tAUGUSTUS\tintron\t7716\t7892\t1\t-\t.\ttranscript_id \"g5.t2\"; gene_id \"g5\";\r\n", "scaffold7_cov100\t19095\t19097\tscaffold7_cov100\tAUGUSTUS\tintron\t18757\t19234\t0.99\t-\t.\ttranscript_id \"g9.t1\"; gene_id \"g9\";\r\n", "scaffold7_cov100\t20228\t20230\tscaffold7_cov100\tAUGUSTUS\tintron\t20129\t20393\t0.8\t+\t.\ttranscript_id \"g11.t1\"; gene_id \"g11\";\r\n", "scaffold7_cov100\t20243\t20245\tscaffold7_cov100\tAUGUSTUS\tintron\t20129\t20393\t0.8\t+\t.\ttranscript_id \"g11.t1\"; gene_id \"g11\";\r\n", "scaffold7_cov100\t20259\t20261\tscaffold7_cov100\tAUGUSTUS\tintron\t20129\t20393\t0.8\t+\t.\ttranscript_id \"g11.t1\"; gene_id \"g11\";\r\n", "\r\n", "==> Meth8_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-sparseMeth.bed-paIntron <==\r\n", "scaffold7_cov100\t13385\t13387\tscaffold7_cov100\tAUGUSTUS\tintron\t13350\t13743\t0.99\t-\t.\ttranscript_id \"g7.t1\"; gene_id \"g7\";\r\n", "scaffold7_cov100\t155682\t155684\tscaffold7_cov100\tAUGUSTUS\tintron\t155667\t155767\t0.4\t-\t.\ttranscript_id \"g41.t1\"; gene_id \"g41\";\r\n", "scaffold7_cov100\t155682\t155684\tscaffold7_cov100\tAUGUSTUS\tintron\t155667\t155767\t0.4\t-\t.\ttranscript_id \"g41.t2\"; gene_id \"g41\";\r\n", "scaffold19_cov103\t112974\t112976\tscaffold19_cov103\tAUGUSTUS\tintron\t112792\t112985\t1\t+\t.\ttranscript_id \"g169.t1\"; gene_id \"g169\";\r\n", "scaffold19_cov103\t112974\t112976\tscaffold19_cov103\tAUGUSTUS\tintron\t112792\t112985\t1\t+\t.\ttranscript_id \"g169.t2\"; gene_id \"g169\";\r\n", "scaffold27_cov99\t85168\t85170\tscaffold27_cov99\tAUGUSTUS\tintron\t85113\t85242\t1\t-\t.\ttranscript_id \"g255.t1\"; gene_id \"g255\";\r\n", "scaffold27_cov99\t85168\t85170\tscaffold27_cov99\tAUGUSTUS\tintron\t85113\t85242\t1\t-\t.\ttranscript_id \"g255.t2\"; gene_id \"g255\";\r\n", "scaffold28_cov97\t792\t794\tscaffold28_cov97\tAUGUSTUS\tintron\t1\t1853\t0.66\t+\t.\ttranscript_id \"g261.t1\"; gene_id \"g261\";\r\n", "scaffold42_cov106\t46883\t46885\tscaffold42_cov106\tAUGUSTUS\tintron\t46864\t46905\t0.8\t-\t.\ttranscript_id \"g373.t1\"; gene_id \"g373\";\r\n", "scaffold42_cov106\t145740\t145742\tscaffold42_cov106\tAUGUSTUS\tintron\t145557\t146755\t0.52\t-\t.\ttranscript_id \"g391.t1\"; gene_id \"g391\";\r\n", "\r\n", "==> Meth8_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-unMeth.bed-paIntron <==\r\n", "scaffold6_cov64\t6338\t6340\tscaffold6_cov64\tAUGUSTUS\tintron\t6268\t6566\t0.58\t+\t.\ttranscript_id \"g2.t1\"; gene_id \"g2\";\r\n", "scaffold6_cov64\t6338\t6340\tscaffold6_cov64\tAUGUSTUS\tintron\t6268\t6566\t0.58\t+\t.\ttranscript_id \"g2.t2\"; gene_id \"g2\";\r\n", "scaffold6_cov64\t6344\t6346\tscaffold6_cov64\tAUGUSTUS\tintron\t6268\t6566\t0.58\t+\t.\ttranscript_id \"g2.t1\"; gene_id \"g2\";\r\n", "scaffold6_cov64\t6344\t6346\tscaffold6_cov64\tAUGUSTUS\tintron\t6268\t6566\t0.58\t+\t.\ttranscript_id \"g2.t2\"; gene_id \"g2\";\r\n", "scaffold6_cov64\t6361\t6363\tscaffold6_cov64\tAUGUSTUS\tintron\t6268\t6566\t0.58\t+\t.\ttranscript_id \"g2.t1\"; gene_id \"g2\";\r\n", "scaffold6_cov64\t6361\t6363\tscaffold6_cov64\tAUGUSTUS\tintron\t6268\t6566\t0.58\t+\t.\ttranscript_id \"g2.t2\"; gene_id \"g2\";\r\n", "scaffold6_cov64\t6374\t6376\tscaffold6_cov64\tAUGUSTUS\tintron\t6268\t6566\t0.58\t+\t.\ttranscript_id \"g2.t1\"; gene_id \"g2\";\r\n", "scaffold6_cov64\t6374\t6376\tscaffold6_cov64\tAUGUSTUS\tintron\t6268\t6566\t0.58\t+\t.\ttranscript_id \"g2.t2\"; gene_id \"g2\";\r\n", "scaffold6_cov64\t6380\t6382\tscaffold6_cov64\tAUGUSTUS\tintron\t6268\t6566\t0.58\t+\t.\ttranscript_id \"g2.t1\"; gene_id \"g2\";\r\n", "scaffold6_cov64\t6380\t6382\tscaffold6_cov64\tAUGUSTUS\tintron\t6268\t6566\t0.58\t+\t.\ttranscript_id \"g2.t2\"; gene_id \"g2\";\r\n", "\r\n", "==> Meth8_R1_001_val_1_bismark_bt2_pe._10x.bedgraph.bed-paIntron <==\r\n", "scaffold6_cov64\t6338\t6340\tscaffold6_cov64\tAUGUSTUS\tintron\t6268\t6566\t0.58\t+\t.\ttranscript_id \"g2.t1\"; gene_id \"g2\";\r\n", "scaffold6_cov64\t6338\t6340\tscaffold6_cov64\tAUGUSTUS\tintron\t6268\t6566\t0.58\t+\t.\ttranscript_id \"g2.t2\"; gene_id \"g2\";\r\n", "scaffold6_cov64\t6344\t6346\tscaffold6_cov64\tAUGUSTUS\tintron\t6268\t6566\t0.58\t+\t.\ttranscript_id \"g2.t1\"; gene_id \"g2\";\r\n", "scaffold6_cov64\t6344\t6346\tscaffold6_cov64\tAUGUSTUS\tintron\t6268\t6566\t0.58\t+\t.\ttranscript_id \"g2.t2\"; gene_id \"g2\";\r\n", "scaffold6_cov64\t6361\t6363\tscaffold6_cov64\tAUGUSTUS\tintron\t6268\t6566\t0.58\t+\t.\ttranscript_id \"g2.t1\"; gene_id \"g2\";\r\n", "scaffold6_cov64\t6361\t6363\tscaffold6_cov64\tAUGUSTUS\tintron\t6268\t6566\t0.58\t+\t.\ttranscript_id \"g2.t2\"; gene_id \"g2\";\r\n", "scaffold6_cov64\t6374\t6376\tscaffold6_cov64\tAUGUSTUS\tintron\t6268\t6566\t0.58\t+\t.\ttranscript_id \"g2.t1\"; gene_id \"g2\";\r\n", "scaffold6_cov64\t6374\t6376\tscaffold6_cov64\tAUGUSTUS\tintron\t6268\t6566\t0.58\t+\t.\ttranscript_id \"g2.t2\"; gene_id \"g2\";\r\n", "scaffold6_cov64\t6380\t6382\tscaffold6_cov64\tAUGUSTUS\tintron\t6268\t6566\t0.58\t+\t.\ttranscript_id \"g2.t1\"; gene_id \"g2\";\r\n", "scaffold6_cov64\t6380\t6382\tscaffold6_cov64\tAUGUSTUS\tintron\t6268\t6566\t0.58\t+\t.\ttranscript_id \"g2.t2\"; gene_id \"g2\";\r\n", "\r\n", "==> Meth9_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-Meth.bed-paIntron <==\r\n", "scaffold7_cov100\t5986\t5988\tscaffold7_cov100\tAUGUSTUS\tintron\t5541\t6090\t1\t-\t.\ttranscript_id \"g4.t1\"; gene_id \"g4\";\r\n", "scaffold7_cov100\t5986\t5988\tscaffold7_cov100\tAUGUSTUS\tintron\t5541\t6090\t1\t-\t.\ttranscript_id \"g4.t2\"; gene_id \"g4\";\r\n", "scaffold7_cov100\t7438\t7440\tscaffold7_cov100\tAUGUSTUS\tintron\t7104\t7649\t1\t-\t.\ttranscript_id \"g5.t1\"; gene_id \"g5\";\r\n", "scaffold7_cov100\t7438\t7440\tscaffold7_cov100\tAUGUSTUS\tintron\t7104\t7649\t1\t-\t.\ttranscript_id \"g5.t2\"; gene_id \"g5\";\r\n", "scaffold7_cov100\t7796\t7798\tscaffold7_cov100\tAUGUSTUS\tintron\t7716\t7892\t1\t-\t.\ttranscript_id \"g5.t1\"; gene_id \"g5\";\r\n", "scaffold7_cov100\t7796\t7798\tscaffold7_cov100\tAUGUSTUS\tintron\t7716\t7892\t1\t-\t.\ttranscript_id \"g5.t2\"; gene_id \"g5\";\r\n", "scaffold7_cov100\t7891\t7892\tscaffold7_cov100\tAUGUSTUS\tintron\t7716\t7892\t1\t-\t.\ttranscript_id \"g5.t1\"; gene_id \"g5\";\r\n", "scaffold7_cov100\t7891\t7892\tscaffold7_cov100\tAUGUSTUS\tintron\t7716\t7892\t1\t-\t.\ttranscript_id \"g5.t2\"; gene_id \"g5\";\r\n", "scaffold7_cov100\t10414\t10416\tscaffold7_cov100\tAUGUSTUS\tintron\t10282\t10594\t1\t-\t.\ttranscript_id \"g6.t1\"; gene_id \"g6\";\r\n", "scaffold7_cov100\t13385\t13387\tscaffold7_cov100\tAUGUSTUS\tintron\t13350\t13743\t0.99\t-\t.\ttranscript_id \"g7.t1\"; gene_id \"g7\";\r\n", "\r\n", "==> Meth9_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-sparseMeth.bed-paIntron <==\r\n", "scaffold6_cov64\t3435\t3437\tscaffold6_cov64\tAUGUSTUS\tintron\t2270\t5582\t0.23\t-\t.\ttranscript_id \"g1.t1\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t3435\t3437\tscaffold6_cov64\tAUGUSTUS\tintron\t2270\t4753\t0.4\t-\t.\ttranscript_id \"g1.t2\"; gene_id \"g1\";\r\n", "scaffold7_cov100\t69268\t69270\tscaffold7_cov100\tAUGUSTUS\tintron\t69212\t69346\t1\t-\t.\ttranscript_id \"g18.t1\"; gene_id \"g18\";\r\n", "scaffold7_cov100\t69313\t69315\tscaffold7_cov100\tAUGUSTUS\tintron\t69212\t69346\t1\t-\t.\ttranscript_id \"g18.t1\"; gene_id \"g18\";\r\n", "scaffold7_cov100\t75920\t75922\tscaffold7_cov100\tAUGUSTUS\tintron\t75809\t76544\t1\t-\t.\ttranscript_id \"g19.t1\"; gene_id \"g19\";\r\n", "scaffold7_cov100\t75963\t75965\tscaffold7_cov100\tAUGUSTUS\tintron\t75809\t76544\t1\t-\t.\ttranscript_id \"g19.t1\"; gene_id \"g19\";\r\n", "scaffold7_cov100\t75972\t75974\tscaffold7_cov100\tAUGUSTUS\tintron\t75809\t76544\t1\t-\t.\ttranscript_id \"g19.t1\"; gene_id \"g19\";\r\n", "scaffold7_cov100\t98616\t98618\tscaffold7_cov100\tAUGUSTUS\tintron\t98271\t98881\t0.46\t-\t.\ttranscript_id \"g24.t2\"; gene_id \"g24\";\r\n", "scaffold7_cov100\t98712\t98714\tscaffold7_cov100\tAUGUSTUS\tintron\t98271\t98881\t0.46\t-\t.\ttranscript_id \"g24.t2\"; gene_id \"g24\";\r\n", "scaffold7_cov100\t114510\t114512\tscaffold7_cov100\tAUGUSTUS\tintron\t114140\t114955\t0.32\t+\t.\ttranscript_id \"g28.t1\"; gene_id \"g28\";\r\n", "\r\n", "==> Meth9_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-unMeth.bed-paIntron <==\r\n", "scaffold6_cov64\t298\t300\tscaffold6_cov64\tAUGUSTUS\tintron\t1\t494\t0.82\t-\t.\ttranscript_id \"g1.t1\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t298\t300\tscaffold6_cov64\tAUGUSTUS\tintron\t1\t494\t0.82\t-\t.\ttranscript_id \"g1.t2\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t489\t491\tscaffold6_cov64\tAUGUSTUS\tintron\t1\t494\t0.82\t-\t.\ttranscript_id \"g1.t1\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t489\t491\tscaffold6_cov64\tAUGUSTUS\tintron\t1\t494\t0.82\t-\t.\ttranscript_id \"g1.t2\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t3412\t3414\tscaffold6_cov64\tAUGUSTUS\tintron\t2270\t5582\t0.23\t-\t.\ttranscript_id \"g1.t1\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t3412\t3414\tscaffold6_cov64\tAUGUSTUS\tintron\t2270\t4753\t0.4\t-\t.\ttranscript_id \"g1.t2\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t3420\t3422\tscaffold6_cov64\tAUGUSTUS\tintron\t2270\t5582\t0.23\t-\t.\ttranscript_id \"g1.t1\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t3420\t3422\tscaffold6_cov64\tAUGUSTUS\tintron\t2270\t4753\t0.4\t-\t.\ttranscript_id \"g1.t2\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t3439\t3441\tscaffold6_cov64\tAUGUSTUS\tintron\t2270\t5582\t0.23\t-\t.\ttranscript_id \"g1.t1\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t3439\t3441\tscaffold6_cov64\tAUGUSTUS\tintron\t2270\t4753\t0.4\t-\t.\ttranscript_id \"g1.t2\"; gene_id \"g1\";\r\n", "\r\n", "==> Meth9_R1_001_val_1_bismark_bt2_pe._10x.bedgraph.bed-paIntron <==\r\n", "scaffold6_cov64\t298\t300\tscaffold6_cov64\tAUGUSTUS\tintron\t1\t494\t0.82\t-\t.\ttranscript_id \"g1.t1\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t298\t300\tscaffold6_cov64\tAUGUSTUS\tintron\t1\t494\t0.82\t-\t.\ttranscript_id \"g1.t2\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t489\t491\tscaffold6_cov64\tAUGUSTUS\tintron\t1\t494\t0.82\t-\t.\ttranscript_id \"g1.t1\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t489\t491\tscaffold6_cov64\tAUGUSTUS\tintron\t1\t494\t0.82\t-\t.\ttranscript_id \"g1.t2\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t3412\t3414\tscaffold6_cov64\tAUGUSTUS\tintron\t2270\t5582\t0.23\t-\t.\ttranscript_id \"g1.t1\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t3412\t3414\tscaffold6_cov64\tAUGUSTUS\tintron\t2270\t4753\t0.4\t-\t.\ttranscript_id \"g1.t2\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t3420\t3422\tscaffold6_cov64\tAUGUSTUS\tintron\t2270\t5582\t0.23\t-\t.\ttranscript_id \"g1.t1\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t3420\t3422\tscaffold6_cov64\tAUGUSTUS\tintron\t2270\t4753\t0.4\t-\t.\ttranscript_id \"g1.t2\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t3435\t3437\tscaffold6_cov64\tAUGUSTUS\tintron\t2270\t5582\t0.23\t-\t.\ttranscript_id \"g1.t1\"; gene_id \"g1\";\r\n", "scaffold6_cov64\t3435\t3437\tscaffold6_cov64\tAUGUSTUS\tintron\t2270\t4753\t0.4\t-\t.\ttranscript_id \"g1.t2\"; gene_id \"g1\";\r\n" ] } ], "source": [ "#Check output\n", "!head *paIntron" ] }, { "cell_type": "code", "execution_count": 110, "metadata": { "scrolled": true }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ " 11164 Meth1_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-Meth.bed-paIntron\n", " 19112 Meth1_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-sparseMeth.bed-paIntron\n", " 703614 Meth1_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-unMeth.bed-paIntron\n", " 733890 Meth1_R1_001_val_1_bismark_bt2_pe._10x.bedgraph.bed-paIntron\n", " 23483 Meth2_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-Meth.bed-paIntron\n", " 32016 Meth2_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-sparseMeth.bed-paIntron\n", " 1181764 Meth2_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-unMeth.bed-paIntron\n", " 1237263 Meth2_R1_001_val_1_bismark_bt2_pe._10x.bedgraph.bed-paIntron\n", " 15720 Meth3_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-Meth.bed-paIntron\n", " 25760 Meth3_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-sparseMeth.bed-paIntron\n", " 867166 Meth3_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-unMeth.bed-paIntron\n", " 908646 Meth3_R1_001_val_1_bismark_bt2_pe._10x.bedgraph.bed-paIntron\n", " 2726 Meth4_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-Meth.bed-paIntron\n", " 16685 Meth4_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-sparseMeth.bed-paIntron\n", " 317025 Meth4_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-unMeth.bed-paIntron\n", " 336436 Meth4_R1_001_val_1_bismark_bt2_pe._10x.bedgraph.bed-paIntron\n", " 3514 Meth5_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-Meth.bed-paIntron\n", " 6409 Meth5_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-sparseMeth.bed-paIntron\n", " 267757 Meth5_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-unMeth.bed-paIntron\n", " 277680 Meth5_R1_001_val_1_bismark_bt2_pe._10x.bedgraph.bed-paIntron\n", " 2348 Meth6_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-Meth.bed-paIntron\n", " 8824 Meth6_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-sparseMeth.bed-paIntron\n", " 276631 Meth6_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-unMeth.bed-paIntron\n", " 287803 Meth6_R1_001_val_1_bismark_bt2_pe._10x.bedgraph.bed-paIntron\n", " 42347 Meth7_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-Meth.bed-paIntron\n", " 15003 Meth7_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-sparseMeth.bed-paIntron\n", " 82993 Meth7_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-unMeth.bed-paIntron\n", " 140343 Meth7_R1_001_val_1_bismark_bt2_pe._10x.bedgraph.bed-paIntron\n", " 27138 Meth8_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-Meth.bed-paIntron\n", " 5541 Meth8_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-sparseMeth.bed-paIntron\n", " 7705 Meth8_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-unMeth.bed-paIntron\n", " 40384 Meth8_R1_001_val_1_bismark_bt2_pe._10x.bedgraph.bed-paIntron\n", " 46592 Meth9_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-Meth.bed-paIntron\n", " 16913 Meth9_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-sparseMeth.bed-paIntron\n", " 83409 Meth9_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-unMeth.bed-paIntron\n", " 146914 Meth9_R1_001_val_1_bismark_bt2_pe._10x.bedgraph.bed-paIntron\n", " 8218718 total\n" ] } ], "source": [ "#Count number of overlaps\n", "!wc -l *paIntron" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "#### 4e. Intergenic" ] }, { "cell_type": "code", "execution_count": 111, "metadata": { "collapsed": true }, "outputs": [], "source": [ "%%bash \n", "\n", "for f in *bed\n", "do\n", " /usr/local/bin/intersectBed \\\n", " -v \\\n", " -a ${f} \\\n", " -b ../../../genome-feature-files/Pact.GFFannotation.Genes.gff \\\n", " > ${f}-paIntergenic\n", "done" ] }, { "cell_type": "code", "execution_count": 112, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "==> Meth1_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-Meth.bed-paIntergenic <==\n", "scaffold7_cov100\t24494\t24496\n", "scaffold7_cov100\t24941\t24943\n", "scaffold7_cov100\t78473\t78475\n", "scaffold7_cov100\t107792\t107794\n", "scaffold7_cov100\t107834\t107836\n", "scaffold7_cov100\t108138\t108140\n", "scaffold7_cov100\t148319\t148321\n", "scaffold7_cov100\t148342\t148344\n", "scaffold7_cov100\t230317\t230319\n", "scaffold7_cov100\t327789\t327791\n", "\n", "==> Meth1_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-sparseMeth.bed-paIntergenic <==\n", "scaffold3_cov83\t475\t477\n", "scaffold3_cov83\t484\t486\n", "scaffold3_cov83\t504\t506\n", "scaffold7_cov100\t24454\t24456\n", "scaffold7_cov100\t25157\t25159\n", "scaffold7_cov100\t31789\t31791\n", "scaffold7_cov100\t121132\t121134\n", "scaffold7_cov100\t163515\t163517\n", "scaffold7_cov100\t194346\t194348\n", "scaffold7_cov100\t196956\t196958\n", "\n", "==> Meth1_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-unMeth.bed-paIntergenic <==\n", "scaffold2_cov51\t649\t651\n", "scaffold2_cov51\t686\t688\n", "scaffold3_cov83\t189\t191\n", "scaffold3_cov83\t208\t210\n", "scaffold3_cov83\t243\t245\n", "scaffold3_cov83\t261\t263\n", "scaffold6_cov64\t5797\t5799\n", "scaffold6_cov64\t5800\t5802\n", "scaffold6_cov64\t6751\t6753\n", "scaffold6_cov64\t6805\t6807\n", "\n", "==> Meth1_R1_001_val_1_bismark_bt2_pe._10x.bedgraph.bed-paIntergenic <==\n", "scaffold2_cov51\t649\t651\n", "scaffold2_cov51\t686\t688\n", "scaffold3_cov83\t189\t191\n", "scaffold3_cov83\t208\t210\n", "scaffold3_cov83\t243\t245\n", "scaffold3_cov83\t261\t263\n", "scaffold3_cov83\t475\t477\n", "scaffold3_cov83\t484\t486\n", "scaffold3_cov83\t504\t506\n", "scaffold6_cov64\t5797\t5799\n", "\n", "==> Meth2_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-Meth.bed-paIntergenic <==\n", "scaffold7_cov100\t6231\t6233\n", "scaffold7_cov100\t6233\t6235\n", "scaffold7_cov100\t12247\t12249\n", "scaffold7_cov100\t13275\t13277\n", "scaffold7_cov100\t19284\t19286\n", "scaffold7_cov100\t19296\t19298\n", "scaffold7_cov100\t24614\t24616\n", "scaffold7_cov100\t24941\t24943\n", "scaffold7_cov100\t24969\t24971\n", "scaffold7_cov100\t77986\t77988\n", "\n", "==> Meth2_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-sparseMeth.bed-paIntergenic <==\n", "scaffold7_cov100\t18520\t18522\n", "scaffold7_cov100\t24895\t24897\n", "scaffold7_cov100\t25157\t25159\n", "scaffold7_cov100\t31808\t31810\n", "scaffold7_cov100\t78386\t78388\n", "scaffold7_cov100\t80016\t80018\n", "scaffold7_cov100\t83659\t83661\n", "scaffold7_cov100\t84872\t84874\n", "scaffold7_cov100\t84995\t84997\n", "scaffold7_cov100\t87017\t87019\n", "\n", "==> Meth2_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-unMeth.bed-paIntergenic <==\n", "scaffold1_cov55\t169\t171\n", "scaffold1_cov55\t194\t196\n", "scaffold1_cov55\t250\t252\n", "scaffold1_cov55\t291\t293\n", "scaffold3_cov83\t189\t191\n", "scaffold3_cov83\t208\t210\n", "scaffold3_cov83\t243\t245\n", "scaffold3_cov83\t261\t263\n", "scaffold3_cov83\t475\t477\n", "scaffold3_cov83\t484\t486\n", "\n", "==> Meth2_R1_001_val_1_bismark_bt2_pe._10x.bedgraph.bed-paIntergenic <==\n", "scaffold1_cov55\t169\t171\n", "scaffold1_cov55\t194\t196\n", "scaffold1_cov55\t250\t252\n", "scaffold1_cov55\t291\t293\n", "scaffold3_cov83\t189\t191\n", "scaffold3_cov83\t208\t210\n", "scaffold3_cov83\t243\t245\n", "scaffold3_cov83\t261\t263\n", "scaffold3_cov83\t475\t477\n", "scaffold3_cov83\t484\t486\n", "\n", "==> Meth3_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-Meth.bed-paIntergenic <==\n", "scaffold7_cov100\t19284\t19286\n", "scaffold7_cov100\t24401\t24403\n", "scaffold7_cov100\t24509\t24511\n", "scaffold7_cov100\t24617\t24619\n", "scaffold7_cov100\t24895\t24897\n", "scaffold7_cov100\t24941\t24943\n", "scaffold7_cov100\t77986\t77988\n", "scaffold7_cov100\t77988\t77990\n", "scaffold7_cov100\t99015\t99017\n", "scaffold7_cov100\t101750\t101752\n", "\n", "==> Meth3_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-sparseMeth.bed-paIntergenic <==\n", "scaffold2_cov51\t686\t688\n", "scaffold3_cov83\t189\t191\n", "scaffold3_cov83\t475\t477\n", "scaffold7_cov100\t24614\t24616\n", "scaffold7_cov100\t24969\t24971\n", "scaffold7_cov100\t25157\t25159\n", "scaffold7_cov100\t49411\t49413\n", "scaffold7_cov100\t49637\t49639\n", "scaffold7_cov100\t82907\t82909\n", "scaffold7_cov100\t82971\t82973\n", "\n", "==> Meth3_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-unMeth.bed-paIntergenic <==\n", "scaffold2_cov51\t649\t651\n", "scaffold2_cov51\t778\t780\n", "scaffold3_cov83\t208\t210\n", "scaffold3_cov83\t243\t245\n", "scaffold3_cov83\t261\t263\n", "scaffold3_cov83\t484\t486\n", "scaffold3_cov83\t504\t506\n", "scaffold6_cov64\t5797\t5799\n", "scaffold6_cov64\t5800\t5802\n", "scaffold6_cov64\t6704\t6706\n", "\n", "==> Meth3_R1_001_val_1_bismark_bt2_pe._10x.bedgraph.bed-paIntergenic <==\n", "scaffold2_cov51\t649\t651\n", "scaffold2_cov51\t686\t688\n", "scaffold2_cov51\t778\t780\n", "scaffold3_cov83\t189\t191\n", "scaffold3_cov83\t208\t210\n", "scaffold3_cov83\t243\t245\n", "scaffold3_cov83\t261\t263\n", "scaffold3_cov83\t475\t477\n", "scaffold3_cov83\t484\t486\n", "scaffold3_cov83\t504\t506\n", "\n", "==> Meth4_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-Meth.bed-paIntergenic <==\n", "scaffold7_cov100\t342219\t342221\n", "scaffold12_cov67\t29992\t29994\n", "scaffold20_cov103\t50562\t50564\n", "scaffold20_cov103\t69200\t69202\n", "scaffold21_cov102\t1879\t1881\n", "scaffold27_cov99\t8577\t8579\n", "scaffold41_cov106\t22329\t22331\n", "scaffold42_cov106\t33801\t33803\n", "scaffold42_cov106\t66341\t66343\n", "scaffold44_cov102\t50648\t50650\n", "\n", "==> Meth4_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-sparseMeth.bed-paIntergenic <==\n", "scaffold6_cov64\t6732\t6734\n", "scaffold7_cov100\t39365\t39367\n", "scaffold7_cov100\t39367\t39369\n", "scaffold7_cov100\t40132\t40134\n", "scaffold7_cov100\t40148\t40150\n", "scaffold7_cov100\t40816\t40818\n", "scaffold7_cov100\t49365\t49367\n", "scaffold7_cov100\t49411\t49413\n", "scaffold7_cov100\t49433\t49435\n", "scaffold7_cov100\t49448\t49450\n", "\n", "==> Meth4_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-unMeth.bed-paIntergenic <==\n", "scaffold6_cov64\t5797\t5799\n", "scaffold6_cov64\t5800\t5802\n", "scaffold6_cov64\t6687\t6689\n", "scaffold6_cov64\t6690\t6692\n", "scaffold6_cov64\t6704\t6706\n", "scaffold6_cov64\t6751\t6753\n", "scaffold6_cov64\t6805\t6807\n", "scaffold6_cov64\t6813\t6815\n", "scaffold6_cov64\t8041\t8043\n", "scaffold6_cov64\t8056\t8058\n", "\n", "==> Meth4_R1_001_val_1_bismark_bt2_pe._10x.bedgraph.bed-paIntergenic <==\n", "scaffold6_cov64\t5797\t5799\n", "scaffold6_cov64\t5800\t5802\n", "scaffold6_cov64\t6687\t6689\n", "scaffold6_cov64\t6690\t6692\n", "scaffold6_cov64\t6704\t6706\n", "scaffold6_cov64\t6732\t6734\n", "scaffold6_cov64\t6751\t6753\n", "scaffold6_cov64\t6805\t6807\n", "scaffold6_cov64\t6813\t6815\n", "scaffold6_cov64\t8041\t8043\n", "\n", "==> Meth5_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-Meth.bed-paIntergenic <==\n", "scaffold7_cov100\t486263\t486265\n", "scaffold12_cov67\t28089\t28091\n", "scaffold19_cov103\t204082\t204084\n", "scaffold19_cov103\t239859\t239861\n", "scaffold20_cov103\t69200\t69202\n", "scaffold20_cov103\t86601\t86603\n", "scaffold28_cov97\t23210\t23212\n", "scaffold28_cov97\t50804\t50806\n", "scaffold41_cov106\t22329\t22331\n", "scaffold41_cov106\t22628\t22630\n", "\n", "==> Meth5_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-sparseMeth.bed-paIntergenic <==\n", "scaffold7_cov100\t131309\t131311\n", "scaffold7_cov100\t162610\t162612\n", "scaffold7_cov100\t191986\t191988\n", "scaffold7_cov100\t218601\t218603\n", "scaffold7_cov100\t344976\t344978\n", "scaffold7_cov100\t384919\t384921\n", "scaffold7_cov100\t457081\t457083\n", "scaffold7_cov100\t479282\t479284\n", "scaffold7_cov100\t498205\t498207\n", "scaffold7_cov100\t507816\t507818\n", "\n", "==> Meth5_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-unMeth.bed-paIntergenic <==\n", "scaffold6_cov64\t5797\t5799\n", "scaffold6_cov64\t5800\t5802\n", "scaffold6_cov64\t6690\t6692\n", "scaffold6_cov64\t6704\t6706\n", "scaffold6_cov64\t6751\t6753\n", "scaffold7_cov100\t3150\t3152\n", "scaffold7_cov100\t3194\t3196\n", "scaffold7_cov100\t3240\t3242\n", "scaffold7_cov100\t3294\t3296\n", "scaffold7_cov100\t3297\t3299\n", "\n", "==> Meth5_R1_001_val_1_bismark_bt2_pe._10x.bedgraph.bed-paIntergenic <==\n", "scaffold6_cov64\t5797\t5799\n", "scaffold6_cov64\t5800\t5802\n", "scaffold6_cov64\t6690\t6692\n", "scaffold6_cov64\t6704\t6706\n", "scaffold6_cov64\t6751\t6753\n", "scaffold7_cov100\t3150\t3152\n", "scaffold7_cov100\t3194\t3196\n", "scaffold7_cov100\t3240\t3242\n", "scaffold7_cov100\t3294\t3296\n", "scaffold7_cov100\t3297\t3299\n", "\n", "==> Meth6_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-Meth.bed-paIntergenic <==\n", "scaffold7_cov100\t281483\t281485\n", "scaffold7_cov100\t507816\t507818\n", "scaffold7_cov100\t507824\t507826\n", "scaffold19_cov103\t94546\t94548\n", "scaffold20_cov103\t69200\t69202\n", "scaffold28_cov97\t23210\t23212\n", "scaffold28_cov97\t50804\t50806\n", "scaffold41_cov106\t22329\t22331\n", "scaffold42_cov106\t38134\t38136\n", "scaffold44_cov102\t50648\t50650\n", "\n", "==> Meth6_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-sparseMeth.bed-paIntergenic <==\n", "scaffold6_cov64\t6704\t6706\n", "scaffold7_cov100\t37936\t37938\n", "scaffold7_cov100\t131309\t131311\n", "scaffold7_cov100\t162610\t162612\n", "scaffold7_cov100\t164670\t164672\n", "scaffold7_cov100\t219436\t219438\n", "scaffold7_cov100\t219440\t219442\n", "scaffold7_cov100\t223230\t223232\n", "scaffold7_cov100\t229665\t229667\n", "scaffold7_cov100\t265131\t265133\n", "\n", "==> Meth6_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-unMeth.bed-paIntergenic <==\n", "scaffold6_cov64\t5797\t5799\n", "scaffold6_cov64\t5800\t5802\n", "scaffold6_cov64\t6690\t6692\n", "scaffold6_cov64\t6751\t6753\n", "scaffold6_cov64\t8041\t8043\n", "scaffold6_cov64\t8056\t8058\n", "scaffold6_cov64\t8070\t8072\n", "scaffold6_cov64\t8079\t8081\n", "scaffold7_cov100\t2834\t2836\n", "scaffold7_cov100\t2904\t2906\n", "\n", "==> Meth6_R1_001_val_1_bismark_bt2_pe._10x.bedgraph.bed-paIntergenic <==\n", "scaffold6_cov64\t5797\t5799\n", "scaffold6_cov64\t5800\t5802\n", "scaffold6_cov64\t6690\t6692\n", "scaffold6_cov64\t6704\t6706\n", "scaffold6_cov64\t6751\t6753\n", "scaffold6_cov64\t8041\t8043\n", "scaffold6_cov64\t8056\t8058\n", "scaffold6_cov64\t8070\t8072\n", "scaffold6_cov64\t8079\t8081\n", "scaffold7_cov100\t2834\t2836\n", "\n", "==> Meth7_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-Meth.bed-paIntergenic <==\n", "scaffold3_cov83\t261\t263\n", "scaffold3_cov83\t475\t477\n", "scaffold3_cov83\t484\t486\n", "scaffold3_cov83\t504\t506\n", "scaffold7_cov100\t6231\t6233\n", "scaffold7_cov100\t6233\t6235\n", "scaffold7_cov100\t12652\t12654\n", "scaffold7_cov100\t12662\t12664\n", "scaffold7_cov100\t12675\t12677\n", "scaffold7_cov100\t12683\t12685\n", "\n", "==> Meth7_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-sparseMeth.bed-paIntergenic <==\n", "scaffold3_cov83\t189\t191\n", "scaffold3_cov83\t208\t210\n", "scaffold7_cov100\t12821\t12823\n", "scaffold7_cov100\t24614\t24616\n", "scaffold7_cov100\t24617\t24619\n", "scaffold7_cov100\t24690\t24692\n", "scaffold7_cov100\t24969\t24971\n", "scaffold7_cov100\t25157\t25159\n", "scaffold7_cov100\t92019\t92021\n", "scaffold7_cov100\t92051\t92053\n", "\n", "==> Meth7_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-unMeth.bed-paIntergenic <==\n", "scaffold3_cov83\t243\t245\n", "scaffold6_cov64\t5797\t5799\n", "scaffold6_cov64\t5800\t5802\n", "scaffold7_cov100\t12587\t12589\n", "scaffold7_cov100\t24830\t24832\n", "scaffold7_cov100\t31606\t31608\n", "scaffold7_cov100\t31645\t31647\n", "scaffold7_cov100\t67512\t67514\n", "scaffold7_cov100\t67517\t67519\n", "scaffold7_cov100\t73414\t73416\n", "\n", "==> Meth7_R1_001_val_1_bismark_bt2_pe._10x.bedgraph.bed-paIntergenic <==\n", "scaffold3_cov83\t189\t191\n", "scaffold3_cov83\t208\t210\n", "scaffold3_cov83\t243\t245\n", "scaffold3_cov83\t261\t263\n", "scaffold3_cov83\t475\t477\n", "scaffold3_cov83\t484\t486\n", "scaffold3_cov83\t504\t506\n", "scaffold6_cov64\t5797\t5799\n", "scaffold6_cov64\t5800\t5802\n", "scaffold7_cov100\t6231\t6233\n", "\n", "==> Meth8_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-Meth.bed-paIntergenic <==\n", "scaffold3_cov83\t475\t477\n", "scaffold7_cov100\t6233\t6235\n", "scaffold7_cov100\t12652\t12654\n", "scaffold7_cov100\t12662\t12664\n", "scaffold7_cov100\t12675\t12677\n", "scaffold7_cov100\t12683\t12685\n", "scaffold7_cov100\t12704\t12706\n", "scaffold7_cov100\t12726\t12728\n", "scaffold7_cov100\t12737\t12739\n", "scaffold7_cov100\t12806\t12808\n", "\n", "==> Meth8_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-sparseMeth.bed-paIntergenic <==\n", "scaffold3_cov83\t484\t486\n", "scaffold7_cov100\t6231\t6233\n", "scaffold7_cov100\t12131\t12133\n", "scaffold7_cov100\t12247\t12249\n", "scaffold7_cov100\t12861\t12863\n", "scaffold7_cov100\t24494\t24496\n", "scaffold7_cov100\t92055\t92057\n", "scaffold7_cov100\t92105\t92107\n", "scaffold7_cov100\t131336\t131338\n", "scaffold7_cov100\t131377\t131379\n", "\n", "==> Meth8_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-unMeth.bed-paIntergenic <==\n", "scaffold7_cov100\t12587\t12589\n", "scaffold7_cov100\t13038\t13040\n", "scaffold7_cov100\t24617\t24619\n", "scaffold7_cov100\t24690\t24692\n", "scaffold7_cov100\t304567\t304569\n", "scaffold7_cov100\t450651\t450653\n", "scaffold7_cov100\t450955\t450957\n", "scaffold7_cov100\t452335\t452337\n", "scaffold7_cov100\t457899\t457901\n", "scaffold18_cov131\t892\t894\n", "\n", "==> Meth8_R1_001_val_1_bismark_bt2_pe._10x.bedgraph.bed-paIntergenic <==\n", "scaffold3_cov83\t475\t477\n", "scaffold3_cov83\t484\t486\n", "scaffold7_cov100\t6231\t6233\n", "scaffold7_cov100\t6233\t6235\n", "scaffold7_cov100\t12131\t12133\n", "scaffold7_cov100\t12247\t12249\n", "scaffold7_cov100\t12587\t12589\n", "scaffold7_cov100\t12652\t12654\n", "scaffold7_cov100\t12662\t12664\n", "scaffold7_cov100\t12675\t12677\n", "\n", "==> Meth9_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-Meth.bed-paIntergenic <==\n", "scaffold7_cov100\t6231\t6233\n", "scaffold7_cov100\t6233\t6235\n", "scaffold7_cov100\t11815\t11817\n", "scaffold7_cov100\t12652\t12654\n", "scaffold7_cov100\t12662\t12664\n", "scaffold7_cov100\t12675\t12677\n", "scaffold7_cov100\t19284\t19286\n", "scaffold7_cov100\t19296\t19298\n", "scaffold7_cov100\t24494\t24496\n", "scaffold7_cov100\t24509\t24511\n", "\n", "==> Meth9_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-sparseMeth.bed-paIntergenic <==\n", "scaffold3_cov83\t189\t191\n", "scaffold3_cov83\t208\t210\n", "scaffold3_cov83\t261\t263\n", "scaffold3_cov83\t475\t477\n", "scaffold3_cov83\t484\t486\n", "scaffold7_cov100\t12683\t12685\n", "scaffold7_cov100\t13275\t13277\n", "scaffold7_cov100\t24614\t24616\n", "scaffold7_cov100\t24617\t24619\n", "scaffold7_cov100\t25157\t25159\n", "\n", "==> Meth9_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-unMeth.bed-paIntergenic <==\n", "scaffold3_cov83\t243\t245\n", "scaffold6_cov64\t5800\t5802\n", "scaffold6_cov64\t6813\t6815\n", "scaffold6_cov64\t6862\t6864\n", "scaffold6_cov64\t6880\t6882\n", "scaffold6_cov64\t6885\t6887\n", "scaffold6_cov64\t6909\t6911\n", "scaffold6_cov64\t7097\t7099\n", "scaffold6_cov64\t7159\t7161\n", "scaffold6_cov64\t7163\t7165\n", "\n", "==> Meth9_R1_001_val_1_bismark_bt2_pe._10x.bedgraph.bed-paIntergenic <==\n", "scaffold3_cov83\t189\t191\n", "scaffold3_cov83\t208\t210\n", "scaffold3_cov83\t243\t245\n", "scaffold3_cov83\t261\t263\n", "scaffold3_cov83\t475\t477\n", "scaffold3_cov83\t484\t486\n", "scaffold6_cov64\t5800\t5802\n", "scaffold6_cov64\t6813\t6815\n", "scaffold6_cov64\t6862\t6864\n", "scaffold6_cov64\t6880\t6882\n" ] } ], "source": [ "#Check output\n", "!head *paIntergenic" ] }, { "cell_type": "code", "execution_count": 113, "metadata": { "scrolled": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ " 11319 Meth1_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-Meth.bed-paIntergenic\n", " 49388 Meth1_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-sparseMeth.bed-paIntergenic\n", " 1278710 Meth1_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-unMeth.bed-paIntergenic\n", " 1339417 Meth1_R1_001_val_1_bismark_bt2_pe._10x.bedgraph.bed-paIntergenic\n", " 18848 Meth2_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-Meth.bed-paIntergenic\n", " 60047 Meth2_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-sparseMeth.bed-paIntergenic\n", " 2028226 Meth2_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-unMeth.bed-paIntergenic\n", " 2107121 Meth2_R1_001_val_1_bismark_bt2_pe._10x.bedgraph.bed-paIntergenic\n", " 15747 Meth3_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-Meth.bed-paIntergenic\n", " 60783 Meth3_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-sparseMeth.bed-paIntergenic\n", " 1526292 Meth3_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-unMeth.bed-paIntergenic\n", " 1602822 Meth3_R1_001_val_1_bismark_bt2_pe._10x.bedgraph.bed-paIntergenic\n", " 7040 Meth4_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-Meth.bed-paIntergenic\n", " 39459 Meth4_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-sparseMeth.bed-paIntergenic\n", " 635371 Meth4_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-unMeth.bed-paIntergenic\n", " 681870 Meth4_R1_001_val_1_bismark_bt2_pe._10x.bedgraph.bed-paIntergenic\n", " 8749 Meth5_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-Meth.bed-paIntergenic\n", " 17176 Meth5_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-sparseMeth.bed-paIntergenic\n", " 550757 Meth5_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-unMeth.bed-paIntergenic\n", " 576682 Meth5_R1_001_val_1_bismark_bt2_pe._10x.bedgraph.bed-paIntergenic\n", " 6335 Meth6_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-Meth.bed-paIntergenic\n", " 23780 Meth6_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-sparseMeth.bed-paIntergenic\n", " 555990 Meth6_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-unMeth.bed-paIntergenic\n", " 586105 Meth6_R1_001_val_1_bismark_bt2_pe._10x.bedgraph.bed-paIntergenic\n", " 107907 Meth7_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-Meth.bed-paIntergenic\n", " 75067 Meth7_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-sparseMeth.bed-paIntergenic\n", " 235852 Meth7_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-unMeth.bed-paIntergenic\n", " 418826 Meth7_R1_001_val_1_bismark_bt2_pe._10x.bedgraph.bed-paIntergenic\n", " 95906 Meth8_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-Meth.bed-paIntergenic\n", " 28006 Meth8_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-sparseMeth.bed-paIntergenic\n", " 37552 Meth8_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-unMeth.bed-paIntergenic\n", " 161464 Meth8_R1_001_val_1_bismark_bt2_pe._10x.bedgraph.bed-paIntergenic\n", " 95913 Meth9_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-Meth.bed-paIntergenic\n", " 78494 Meth9_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-sparseMeth.bed-paIntergenic\n", " 236207 Meth9_R1_001_val_1_bismark_bt2_pe._10x.bedgraph-unMeth.bed-paIntergenic\n", " 410614 Meth9_R1_001_val_1_bismark_bt2_pe._10x.bedgraph.bed-paIntergenic\n", " 15769842 total\n" ] } ], "source": [ "#Count number of overlaps\n", "!wc -l *paIntergenic" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "#### Summary" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "##### Overlaps with Genes\n", "\n", "| **Sample** \t| **Method** \t| **CpG with Data** \t| **Methylated CpG** \t| **Sparsely Methylated CpG** \t| **Unmethylated CpG** \t|\n", "|------------\t|------------\t|-------------------\t|--------------------\t|-----------------------------\t|----------------------\t|\n", "| 1 \t| WGBS \t| 1179434 \t| 25899 (2.2%) \t| 34626 (2.9%) \t| 1118909 (94.9%) \t|\n", "| 2 \t| WGBS \t| 1821034 \t| 47716 (2.6%) \t| 49984 (2.7%) \t| 1723334 (94.6%) \t|\n", "| 3 \t| WGBS \t| 1426087 \t| 35357 (2.5%) \t| 44108 (3.1%) \t| 1346622 (94.4%) \t|\n", "| 4 \t| RRBS \t| 502813 \t| 4988 (1.0%) \t| 26205 (5.2%) \t| 471620 (93.8%) \t|\n", "| 5 \t| RRBS \t| 416016 \t| 5815 (1.4%) \t| 10664 (2.6%) \t| 399537 (96.0%) \t|\n", "| 6 \t| RRBS \t| 428818 \t| 4293 (1.0%) \t| 14614 (3.4%) \t| 409911 (95.6%) \t|\n", "| 7 \t| MBD-BSSeq \t| 325489 \t| 87468 (26.9%) \t| 31803 (9.8%) \t| 206218 (63.4%) \t|\n", "| 8 \t| MBD-BSSeq \t| 88675 \t| 60278 (68.0%) \t| 11894 (13.4%) \t| 16503 (18.6%) \t|\n", "| 9 \t| MBD-BSSeq \t| 314739 \t| 92131 (29.3%) \t| 34146 (10.8%) \t| 188462 (59.9%) \t|" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "##### Overlaps with Coding Sequences (CDS)\n", "\n", "| **Sample** \t| **Method** \t| **CpG with Data** \t| **Methylated CpG** \t| **Sparsely Methylated CpG** \t| **Unmethylated CpG** \t|\n", "|------------\t|------------\t|-------------------\t|--------------------\t|-----------------------------\t|----------------------\t|\n", "| 1 \t| WGBS \t| 850489 \t| 23872 (2.8%) \t| 26408 (3.1%) \t| 800209 (94.1%) \t|\n", "| 2 \t| WGBS \t| 1219826 \t| 41839 (3.4%) \t| 34947 (2.9%) \t| 1143040 (93.7%) \t|\n", "| 3 \t| WGBS \t| 1010637 \t| 32069 (3.2%) \t| 32550 (3.2%) \t| 946018 (93.6%) \t|\n", "| 4 \t| RRBS \t| 334839 \t| 3840 (1.1%) \t| 18125 (5.4%) \t| 312874 (93.4%) \t|\n", "| 5 \t| RRBS \t| 275416 \t| 4217 (1.5%) \t| 7617 (2.8%) \t| 263582 (95.7%) \t|\n", "| 6 \t| RRBS \t| 283255 \t| 3230 (1.1%) \t| 10420 (3.7%) \t| 269605 (95.2%) \t|\n", "| 7 \t| MBD-BSSeq \t| 284856 \t| 72744 (25.5%) \t| 24809 (8.7%) \t| 187303 (65.8%) \t|\n", "| 8 \t| MBD-BSSeq \t| 73240 \t| 51129 (69.8%) \t| 9109 (12.4%) \t| 13002 (17.8%) \t|\n", "| 9 \t| MBD-BSSeq \t| 265810 \t| 75705 (28.5%) \t| 26175 (9.8%) \t| 163930 (61.7%) \t|" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "##### Overalps with Introns\n", "\n", "| **Sample** \t| **Method** \t| **CpG with Data** \t| **Methylated CpG** \t| **Sparsely Methylated CpG** \t| **Unmethylated CpG** \t|\n", "|------------\t|------------\t|-------------------\t|--------------------\t|-----------------------------\t|----------------------\t|\n", "| 1 \t| WGBS \t| 733890 \t| 11164 (1.5%) \t| 19112 (2.6%) \t| 703614 (95.9%) \t|\n", "| 2 \t| WGBS \t| 1237263 \t| 23483 (1.9%) \t| 32016 (2.6%) \t| 1181764 (95.5%) \t|\n", "| 3 \t| WGBS \t| 908646 \t| 15720 (1.7%) \t| 25760 (2.8%) \t| 867166 (95.4%) \t|\n", "| 4 \t| RRBS \t| 336436 \t| 2726 (0.8%) \t| 16685 (5.0%) \t| 317025 (94.2%) \t|\n", "| 5 \t| RRBS \t| 277680 \t| 3514 (1.3%) \t| 6409 (2.3%) \t| 267757 (96.4%) \t|\n", "| 6 \t| RRBS \t| 287803 \t| 2348 (0.8%) \t| 8824 (3.1%) \t| 276631 (96.1%) \t|\n", "| 7 \t| MBD-BSSeq \t| 140343 \t| 42347 (30.2%) \t| 15003 (10.7%) \t| 82993 (59.1%) \t|\n", "| 8 \t| MBD-BSSeq \t| 40384 \t| 27138 (67.2%) \t| 5541 (13.7%) \t| 7705 (19.1%) \t|\n", "| 9 \t| MBD-BSSeq \t| 146914 \t| 46592 (31.7%) \t| 16913 (11.5%) \t| 83409 (56.8%) \t|" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "##### Overlaps with Integenic regions\n", "\n", "| **Sample** \t| **Method** \t| **CpG with Data** \t| **Methylated CpG** \t| **Sparsely Methylated CpG** \t| **Unmethylated CpG** \t|\n", "|------------\t|------------\t|-------------------\t|--------------------\t|-----------------------------\t|----------------------\t|\n", "| 1 \t| WGBS \t| 1339417 \t| 11319 (0.8%) \t| 49388 (3.7%) \t| 1278710 (95.5%) \t|\n", "| 2 \t| WGBS \t| 2107121 \t| 18848 (0.9%) \t| 60047 (2.8%) \t| 2028226 (96.3%) \t|\n", "| 3 \t| WGBS \t| 1602822 \t| 15747 (1.0%) \t| 60783 (3.8%) \t| 1526292 (95.2%) \t|\n", "| 4 \t| RRBS \t| 681870 \t| 7040 (1.0%) \t| 39459 (5.8%) \t| 635371 (93.2%) \t|\n", "| 5 \t| RRBS \t| 576682 \t| 8749 (1.5%) \t| 17176 (3.0%) \t| 550757 (95.5%) \t|\n", "| 6 \t| RRBS \t| 586105 \t| 6335 (1.1%) \t| 23780 (4.1%) \t| 555990 (94.9%) \t|\n", "| 7 \t| MBD-BSSeq \t| 418826 \t| 107907 (25.8%) \t| 75067 (17.9%) \t| 235852 (56.3%) \t|\n", "| 8 \t| MBD-BSSeq \t| 161464 \t| 95906 (59.4%) \t| 28006 (17.3%) \t| 37552 (23.3%) \t|\n", "| 9 \t| MBD-BSSeq \t| 410614 \t| 95913 (23.4%) \t| 78494 (19.1%) \t| 236207 (57.5%) \t|" ] }, { "cell_type": "code", "execution_count": null, "metadata": { "collapsed": true }, "outputs": [], "source": [] } ], "metadata": { "anaconda-cloud": {}, "kernelspec": { "display_name": "Python 3", "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": "3.7.4" } }, "nbformat": 4, "nbformat_minor": 2 }