{ "metadata": { "name": "", "signature": "sha256:4d1623be9ff680d79e49f2872da87d5ec687f5ef1276eb44b402ac77db52370c" }, "nbformat": 3, "nbformat_minor": 0, "worksheets": [ { "cells": [ { "cell_type": "heading", "level": 1, "metadata": {}, "source": [ "BSMAP-methatio-feature track\n" ] }, { "cell_type": "code", "collapsed": false, "input": [ "#trying to get clean version\n", "!date " ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ "Sun Mar 16 04:32:55 PDT 2014\r\n" ] } ], "prompt_number": 81 }, { "cell_type": "heading", "level": 2, "metadata": {}, "source": [ "Concatenate technical replicates " ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "September is known as FCD2CA8: November Core ID FCC39EM\n", "\n" ] }, { "cell_type": "heading", "level": 4, "metadata": {}, "source": [ "M1" ] }, { "cell_type": "code", "collapsed": false, "input": [ "#Will go September then Novemeber\n", "!cat /Volumes/web/trilobite/Crassostrea_gigas_HTSdata/batterbox/FCD2CA8_2/Sample_BS_CgM1/filtered_BS_CgM1_ACTTGA_L007_R1.fastq \\\n", "/Volumes/web/trilobite/Crassostrea_gigas_HTSdata/batterbox/FCC39EM_02/FCC39EM/Sample_BS_CgM1/filtered_BS_CgM1_ACTTGA_L004_R1.fastq > \\\n", "/Volumes/web/cnidarian/BiGo_larvae_merge/CgM1_R1a.fastq \\" ], "language": "python", "metadata": {}, "outputs": [], "prompt_number": 11 }, { "cell_type": "code", "collapsed": false, "input": [ "!cat /Volumes/web/trilobite/Crassostrea_gigas_HTSdata/batterbox/FCD2CA8_2/Sample_BS_CgM1/filtered_BS_CgM1_ACTTGA_L007_R2.fastq \\\n", "/Volumes/web/trilobite/Crassostrea_gigas_HTSdata/batterbox/FCC39EM_02/FCC39EM/Sample_BS_CgM1/filtered_BS_CgM1_ACTTGA_L004_R2.fastq > \\\n", "/Volumes/web/cnidarian/BiGo_larvae_merge/CgM1_R2a.fastq \\" ], "language": "python", "metadata": {}, "outputs": [], "prompt_number": 12 }, { "cell_type": "heading", "level": 4, "metadata": {}, "source": [ "M3" ] }, { "cell_type": "code", "collapsed": false, "input": [ "R1_A8=\"/Volumes/web/trilobite/Crassostrea_gigas_HTSdata/batterbox/FCD2CA8_2/Sample_BS_CgM3/filtered_BS_CgM3_GATCAG_L007_R1.fastq\"\n", "R1_EM=\"/Volumes/web/trilobite/Crassostrea_gigas_HTSdata/batterbox/FCC39EM_02/FCC39EM/Sample_BS_CgM3/filtered_BS_CgM3_GATCAG_L004_R1.fastq\"\n", " \n", "R2_A8=\"/Volumes/web/trilobite/Crassostrea_gigas_HTSdata/batterbox/FCD2CA8_2/Sample_BS_CgM3/filtered_BS_CgM3_GATCAG_L007_R2.fastq\"\n", "R2_EM=\"/Volumes/web/trilobite/Crassostrea_gigas_HTSdata/batterbox/FCC39EM_02/FCC39EM/Sample_BS_CgM3/filtered_BS_CgM3_GATCAG_L004_R2.fastq\"" ], "language": "python", "metadata": {}, "outputs": [], "prompt_number": 20 }, { "cell_type": "code", "collapsed": false, "input": [ "!cat {R1_A8} \\\n", "{R1_EM} > \\\n", "/Volumes/web/cnidarian/BiGo_larvae_merge/CgM3_R1a.fastq \\" ], "language": "python", "metadata": {}, "outputs": [], "prompt_number": 21 }, { "cell_type": "code", "collapsed": false, "input": [ "!cat {R2_A8} \\\n", "{R2_EM} > \\\n", "/Volumes/web/cnidarian/BiGo_larvae_merge/CgM3_R2a.fastq \\" ], "language": "python", "metadata": {}, "outputs": [], "prompt_number": 22 }, { "cell_type": "heading", "level": 4, "metadata": {}, "source": [ "T1D3" ] }, { "cell_type": "code", "collapsed": false, "input": [ "sample=\"T1D3\"" ], "language": "python", "metadata": {}, "outputs": [], "prompt_number": 23 }, { "cell_type": "code", "collapsed": false, "input": [ "!gunzip /Volumes/web/trilobite/Crassostrea_gigas_HTSdata/batterbox/FCC39EM_02/FCC39EM/Sample_BS_CgLarv_T1D3/filtered_BS_CgLarv_T1D3_TGACCA_L004_R1.fastq.gz" ], "language": "python", "metadata": {}, "outputs": [], "prompt_number": 13 }, { "cell_type": "code", "collapsed": false, "input": [ "!gunzip /Volumes/web/trilobite/Crassostrea_gigas_HTSdata/batterbox/FCC39EM_02/FCC39EM/Sample_BS_CgLarv_T1D3/filtered_BS_CgLarv_T1D3_TGACCA_L004_R2.fastq.gz" ], "language": "python", "metadata": {}, "outputs": [], "prompt_number": 14 }, { "cell_type": "code", "collapsed": false, "input": [ "R1_A8=\"/Volumes/web/trilobite/Crassostrea_gigas_HTSdata/batterbox/FCD2CA8_2/Sample_BS_CgLarv_T1D3/filtered_BS_CgLarv_T1D3_TGACCA_L007_R1.fastq\"\n", "R1_EM=\"/Volumes/web/trilobite/Crassostrea_gigas_HTSdata/batterbox/FCC39EM_02/FCC39EM/Sample_BS_CgLarv_T1D3/filtered_BS_CgLarv_T1D3_TGACCA_L004_R1.fastq\"\n", " \n", "R2_A8=\"/Volumes/web/trilobite/Crassostrea_gigas_HTSdata/batterbox/FCD2CA8_2/Sample_BS_CgLarv_T1D3/filtered_BS_CgLarv_T1D3_TGACCA_L007_R2.fastq\"\n", "R2_EM=\"/Volumes/web/trilobite/Crassostrea_gigas_HTSdata/batterbox/FCC39EM_02/FCC39EM/Sample_BS_CgLarv_T1D3/filtered_BS_CgLarv_T1D3_TGACCA_L004_R2.fastq\"" ], "language": "python", "metadata": {}, "outputs": [], "prompt_number": 24 }, { "cell_type": "code", "collapsed": false, "input": [ "!cat {R1_A8} \\\n", "{R1_EM} > \\\n", "/Volumes/web/cnidarian/BiGo_larvae_merge/Cg{sample}_R1a.fastq \\\n", "\n" ], "language": "python", "metadata": {}, "outputs": [], "prompt_number": 25 }, { "cell_type": "code", "collapsed": false, "input": [ "!cat {R2_A8} \\\n", "{R2_EM} > \\\n", "/Volumes/web/cnidarian/BiGo_larvae_merge/Cg{sample}_R2a.fastq \\" ], "language": "python", "metadata": {}, "outputs": [], "prompt_number": 26 }, { "cell_type": "heading", "level": 4, "metadata": {}, "source": [ "T1D5" ] }, { "cell_type": "code", "collapsed": false, "input": [ "!gunzip /Volumes/web/trilobite/Crassostrea_gigas_HTSdata/batterbox/FCD2CA8_2/Sample_BS_CgLarv_T1D5/filtered_BS_CgLarv_T1D5_ACAGTG_L007_R1.fastq.gz" ], "language": "python", "metadata": {}, "outputs": [] }, { "cell_type": "code", "collapsed": false, "input": [ "!gunzip /Volumes/web/trilobite/Crassostrea_gigas_HTSdata/batterbox/FCD2CA8_2/Sample_BS_CgLarv_T1D5/filtered_BS_CgLarv_T1D5_ACAGTG_L007_R2.fastq.gz" ], "language": "python", "metadata": {}, "outputs": [], "prompt_number": 29 }, { "cell_type": "code", "collapsed": false, "input": [ "!gunzip /Volumes/web/trilobite/Crassostrea_gigas_HTSdata/batterbox/FCC39EM_02/FCC39EM/Sample_BS_CgLarv_T1D5/filtered_BS_CgLarv_T1D5_ACAGTG_L004_R1.fastq.gz" ], "language": "python", "metadata": {}, "outputs": [], "prompt_number": 31 }, { "cell_type": "code", "collapsed": false, "input": [ "!gunzip /Volumes/web/trilobite/Crassostrea_gigas_HTSdata/batterbox/FCC39EM_02/FCC39EM/Sample_BS_CgLarv_T1D5/filtered_BS_CgLarv_T1D5_ACAGTG_L004_R2.fastq.gz" ], "language": "python", "metadata": {}, "outputs": [], "prompt_number": 32 }, { "cell_type": "code", "collapsed": false, "input": [ "R1_A8=\"/Volumes/web/trilobite/Crassostrea_gigas_HTSdata/batterbox/FCD2CA8_2/Sample_BS_CgLarv_T1D5/filtered_BS_CgLarv_T1D5_ACAGTG_L007_R1.fastq\"\n", "R1_EM=\"/Volumes/web/trilobite/Crassostrea_gigas_HTSdata/batterbox/FCC39EM_02/FCC39EM/Sample_BS_CgLarv_T1D5/filtered_BS_CgLarv_T1D5_ACAGTG_L004_R1.fastq\"\n", " \n", "R2_A8=\"/Volumes/web/trilobite/Crassostrea_gigas_HTSdata/batterbox/FCD2CA8_2/Sample_BS_CgLarv_T1D5/filtered_BS_CgLarv_T1D5_ACAGTG_L007_R2.fastq\"\n", "R2_EM=\"/Volumes/web/trilobite/Crassostrea_gigas_HTSdata/batterbox/FCC39EM_02/FCC39EM/Sample_BS_CgLarv_T1D5/filtered_BS_CgLarv_T1D5_ACAGTG_L004_R2.fastq\"" ], "language": "python", "metadata": {}, "outputs": [], "prompt_number": 33 }, { "cell_type": "code", "collapsed": false, "input": [ "sample=\"T1D5\"" ], "language": "python", "metadata": {}, "outputs": [], "prompt_number": 34 }, { "cell_type": "code", "collapsed": false, "input": [ "!cat {R1_A8} \\\n", "{R1_EM} > \\\n", "/Volumes/web/cnidarian/BiGo_larvae_merge/Cg{sample}_R1a.fastq \\\n" ], "language": "python", "metadata": {}, "outputs": [], "prompt_number": 35 }, { "cell_type": "code", "collapsed": false, "input": [ "!cat {R2_A8} \\\n", "{R2_EM} > \\\n", "/Volumes/web/cnidarian/BiGo_larvae_merge/Cg{sample}_R2a.fastq \\" ], "language": "python", "metadata": {}, "outputs": [], "prompt_number": 36 }, { "cell_type": "heading", "level": 4, "metadata": {}, "source": [ "T3D3" ] }, { "cell_type": "code", "collapsed": false, "input": [ "!gunzip /Volumes/web/trilobite/Crassostrea_gigas_HTSdata/batterbox/FCD2CA8_2/Sample_Bs_CgLarve_T3D3/filtered_Bs_CgLarve_T3D3_GCCAAT_L007*" ], "language": "python", "metadata": {}, "outputs": [], "prompt_number": 51 }, { "cell_type": "code", "collapsed": false, "input": [ "!gunzip /Volumes/web/trilobite/Crassostrea_gigas_HTSdata/batterbox/FCC39EM_02/FCC39EM/Sample_Bs_CgLarve_T3D3/filtered_Bs_CgLarve_T3D3_GCCAAT_L004*" ], "language": "python", "metadata": {}, "outputs": [] }, { "cell_type": "code", "collapsed": false, "input": [ "R1_A8=\"/Volumes/web/trilobite/Crassostrea_gigas_HTSdata/batterbox/FCD2CA8_2/Sample_Bs_CgLarve_T3D3/filtered_Bs_CgLarve_T3D3_GCCAAT_L007_R1.fastq\"\n", "R1_EM=\"/Volumes/web/trilobite/Crassostrea_gigas_HTSdata/batterbox/FCC39EM_02/FCC39EM/Sample_Bs_CgLarve_T3D3/filtered_Bs_CgLarve_T3D3_GCCAAT_L004_R1.fastq\"\n", " \n", "R2_A8=\"/Volumes/web/trilobite/Crassostrea_gigas_HTSdata/batterbox/FCD2CA8_2/Sample_Bs_CgLarve_T3D3/filtered_Bs_CgLarve_T3D3_GCCAAT_L007_R2.fastq\"\n", "R2_EM=\"/Volumes/web/trilobite/Crassostrea_gigas_HTSdata/batterbox/FCC39EM_02/FCC39EM/Sample_Bs_CgLarve_T3D3/filtered_Bs_CgLarve_T3D3_GCCAAT_L004_R2.fastq\"" ], "language": "python", "metadata": {}, "outputs": [], "prompt_number": 58 }, { "cell_type": "code", "collapsed": false, "input": [ "sample=\"T3D3\"" ], "language": "python", "metadata": {}, "outputs": [], "prompt_number": 59 }, { "cell_type": "code", "collapsed": false, "input": [ "!cat {R1_A8} \\\n", "{R1_EM} > \\\n", "/Volumes/web/cnidarian/BiGo_larvae_merge/Cg{sample}_R1a.fastq \\\n" ], "language": "python", "metadata": {}, "outputs": [], "prompt_number": 60 }, { "cell_type": "code", "collapsed": false, "input": [ "!cat {R2_A8} \\\n", "{R2_EM} > \\\n", "/Volumes/web/cnidarian/BiGo_larvae_merge/Cg{sample}_R2a.fastq \\" ], "language": "python", "metadata": {}, "outputs": [], "prompt_number": 61 }, { "cell_type": "heading", "level": 4, "metadata": {}, "source": [ "T3D5" ] }, { "cell_type": "code", "collapsed": false, "input": [ "!gunzip /Volumes/web/trilobite/Crassostrea_gigas_HTSdata/batterbox/FCD2CA8_2/Sample_BS_CgLarv_T3D5/filtered_*" ], "language": "python", "metadata": {}, "outputs": [], "prompt_number": 38 }, { "cell_type": "code", "collapsed": false, "input": [ "!gunzip /Volumes/web/trilobite/Crassostrea_gigas_HTSdata/batterbox/FCC39EM_02/FCC39EM/Sample_BS_CgLarv_T3D5/filtered_*" ], "language": "python", "metadata": {}, "outputs": [], "prompt_number": 39 }, { "cell_type": "code", "collapsed": false, "input": [ "R1_A8=\"/Volumes/web/trilobite/Crassostrea_gigas_HTSdata/batterbox/FCD2CA8_2/Sample_BS_CgLarv_T3D5/filtered_BS_CgLarv_T3D5_CAGATC_L007_R1.fastq\"\n", "R1_EM=\"/Volumes/web/trilobite/Crassostrea_gigas_HTSdata/batterbox/FCC39EM_02/FCC39EM/Sample_BS_CgLarv_T3D5/filtered_BS_CgLarv_T3D5_CAGATC_L004_R1.fastq\"\n", " \n", "R2_A8=\"/Volumes/web/trilobite/Crassostrea_gigas_HTSdata/batterbox/FCD2CA8_2/Sample_BS_CgLarv_T3D5/filtered_BS_CgLarv_T3D5_CAGATC_L007_R2.fastq\"\n", "R2_EM=\"/Volumes/web/trilobite/Crassostrea_gigas_HTSdata/batterbox/FCC39EM_02/FCC39EM/Sample_BS_CgLarv_T3D5/filtered_BS_CgLarv_T3D5_CAGATC_L004_R2.fastq\"" ], "language": "python", "metadata": {}, "outputs": [], "prompt_number": 40 }, { "cell_type": "code", "collapsed": false, "input": [ "sample=\"T3D5\"" ], "language": "python", "metadata": {}, "outputs": [], "prompt_number": 41 }, { "cell_type": "code", "collapsed": false, "input": [ "!cat {R1_A8} \\\n", "{R1_EM} > \\\n", "/Volumes/web/cnidarian/BiGo_larvae_merge/Cg{sample}_R1a.fastq \\\n" ], "language": "python", "metadata": {}, "outputs": [], "prompt_number": 42 }, { "cell_type": "code", "collapsed": false, "input": [ "!cat {R2_A8} \\\n", "{R2_EM} > \\\n", "/Volumes/web/cnidarian/BiGo_larvae_merge/Cg{sample}_R2a.fastq \\" ], "language": "python", "metadata": {}, "outputs": [] }, { "cell_type": "heading", "level": 2, "metadata": {}, "source": [ "BSMAP" ] }, { "cell_type": "code", "collapsed": false, "input": [ "#file ID\n", "fid=\"CgM1\"\n", "\n", "#TIMESTAMP\n", "date=!date +%m%d_%H%M\n", "\n", "#working directory (parent)\n", "wd='/Volumes/web/cnidarian/BiGo_larvae_merge/'\n", "\n", "#where is bsmap\n", "#bsmap=\"/Users/Shared/Apps/bsmap-2.73/\"\n", "bsmap=\"/Volumes/Bay3/Software/BSMAP/bsmap-2.74/\"\n", "\n", "#genome file \n", "genome=\"/Volumes/web/whale/ensembl/ftp.ensemblgenomes.org/pub/release-21/metazoa/fasta/crassostrea_gigas/dna/Crassostrea_gigas.GCA_000297895.1.21.dna_sm.genome.fa\"" ], "language": "python", "metadata": {}, "outputs": [], "prompt_number": 1 }, { "cell_type": "code", "collapsed": false, "input": [ "cd {wd} \n" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ "/Volumes/web/cnidarian/BiGo_larvae_merge\n" ] } ], "prompt_number": 2 }, { "cell_type": "code", "collapsed": false, "input": [ "mkdir {fid}_{date} \n" ], "language": "python", "metadata": {}, "outputs": [], "prompt_number": 3 }, { "cell_type": "code", "collapsed": false, "input": [ "cd {fid}_{date} " ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ "/Volumes/web/cnidarian/BiGo_larvae_merge/CgM1_[0316_0954]\n" ] } ], "prompt_number": 4 }, { "cell_type": "code", "collapsed": false, "input": [ "#option - number of processes \n", "!{bsmap}bsmap -a {wd}{fid}_R1a.fastq -b {wd}{fid}_R2a.fastq -d {genome} -o bsmap_out.sam -p 4 \n", "!python {bsmap}methratio.py -d {genome} -u -z -g -o methratio_out.txt -s {bsmap}samtools bsmap_out.sam \n", "#command for only obtaining the context '__CG_'\n", "!grep \"[A-Z][A-Z]CG[A-Z]\" methratio_out_CG.txt \n", "#5x coverage\n", "!awk '{if ($8 >= 5) print $1,$2-1,$2+1,\"CpG\",$5}' filt_methratio_out_CG.igv \n", "!tr ' ' \"\\t\" filt_methratio_{fid}.igv\n" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ "\r\n", "BSMAP v2.74\r\n", "Start at: Sun Mar 16 09:54:25 2014\r\n", "\r\n", "Input reference file: /Volumes/web/whale/ensembl/ftp.ensemblgenomes.org/pub/release-21/metazoa/fasta/crassostrea_gigas/dna/Crassostrea_gigas.GCA_000297895.1.21.dna_sm.genome.fa \t(format: FASTA)\r\n" ] }, { "output_type": "stream", "stream": "stdout", "text": [ "Load in 7658 db seqs, total size 557717710 bp. 13 secs passed\r\n", "total_kmers: 43046721\r\n" ] }, { "output_type": "stream", "stream": "stdout", "text": [ "Create seed table. 55 secs passed\r\n", "max number of mismatches: read_length * 8% \tmax gap size: 0\r\n", "kmer cut-off ratio: " ] }, { "output_type": "stream", "stream": "stdout", "text": [ "5e-07\r\n", "max multi-hits: 100\tmax Ns: 5\tseed size: 16\tindex interval: 4\r\n", "quality cutoff: 0\tbase quality char: '!'\r\n", "min fragment size:28\tmax fragemt size:500\r\n", "start from read #1\tend at read #4294967295\r\n", "additional alignment: T in reads => C in reference\r\n", "mapping strand (read_1): ++,-+\r\n", "mapping strand (read_2): +-,--\r\n", "Pair-end alignment(4 threads)\r\n", "Input read file #1: /Volumes/web/cnidarian/BiGo_larvae_merge/CgM1_R1a.fastq \t(format: FASTQ)\r\n", "Input read file #2: /Volumes/web/cnidarian/BiGo_larvae_merge/CgM1_R2a.fastq \t(format: FASTQ)\r\n", "Output file: bsmap_out.sam\t (format: SAM)\r\n" ] }, { "output_type": "stream", "stream": "stdout", "text": [ "Thread #0: \t150000 read pairs finished. 98 secs passed\r\n" ] }, { "output_type": "stream", "stream": "stdout", "text": [ "Thread #3: \t200000 read pairs finished. 98 secs passed\r\n" ] }, { "output_type": "stream", "stream": "stdout", "text": [ "Thread #1: \t100000 read pairs finished. 98 secs passed\r\n" ] }, { "output_type": "stream", "stream": 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"stream", "stream": "stdout", "text": [ "@ Sun Mar 16 10:22:36 2014: reading reference /Volumes/web/whale/ensembl/ftp.ensemblgenomes.org/pub/release-21/metazoa/fasta/crassostrea_gigas/dna/Crassostrea_gigas.GCA_000297895.1.21.dna_sm.genome.fa ...\r\n" ] }, { "output_type": "stream", "stream": "stdout", "text": [ "@ Sun Mar 16 10:23:28 2014: reading bsmap_out.sam ...\r\n" ] }, { "output_type": "stream", "stream": "stdout", "text": [ "[samopen] SAM header is present: 7658 sequences.\r\n" ] }, { "output_type": "stream", "stream": "stdout", "text": [ "\t@ Sun Mar 16 10:31:20 2014: read 10000000 lines\r\n" ] }, { "output_type": "stream", "stream": "stdout", "text": [ "@ Sun Mar 16 10:31:49 2014: combining CpG methylation from both strands ...\r\n" ] }, { "output_type": "stream", "stream": "stdout", "text": [ "@ Sun Mar 16 10:32:31 2014: writing methratio_out.txt ...\r\n" ] }, { "output_type": "stream", "stream": "stdout", "text": [ "@ Sun Mar 16 10:47:08 2014: done.\r\n", "total 8562355 valid mappings, 48968967 covered cytosines, average coverage: 1.80 fold.\r\n" ] } ], "prompt_number": 5 }, { "cell_type": "code", "collapsed": false, "input": [ "!head filt_methratio_{fid}.igv" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ "C12768\t102\t104\tCpG\t0.167\r\n", "C12806\t141\t143\tCpG\t0.333\r\n", "C12924\t29\t31\tCpG\t0.000\r\n", "C12924\t37\t39\tCpG\t0.000\r\n", "C12924\t51\t53\tCpG\t0.000\r\n", "C12924\t59\t61\tCpG\t0.000\r\n", "C12924\t126\t128\tCpG\t0.000\r\n", "C12924\t135\t137\tCpG\t0.000\r\n", "C13128\t86\t88\tCpG\t0.000\r\n", "C13208\t82\t84\tCpG\t0.400\r\n" ] } ], "prompt_number": 6 }, { "cell_type": "code", "collapsed": false, "input": [ "#file ID\n", "fid=\"CgM3\"\n", "\n", "#TIMESTAMP\n", "date=!date +%m%d_%H%M\n", "\n", "#working directory (parent)\n", "wd='/Volumes/web/cnidarian/BiGo_larvae_merge/'" ], "language": "python", "metadata": {}, "outputs": [], "prompt_number": 8 }, { "cell_type": "code", "collapsed": false, "input": [ "cd {wd}\n" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ "/Volumes/web/cnidarian/BiGo_larvae_merge\n" ] } ], "prompt_number": 10 }, { "cell_type": "code", "collapsed": false, "input": [ "mkdir {fid}_{date}\n" ], "language": "python", "metadata": {}, "outputs": [], "prompt_number": 12 }, { "cell_type": "code", "collapsed": false, "input": [ "cd {fid}_{date}" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ "/Volumes/web/cnidarian/BiGo_larvae_merge/CgM3_[0316_1207]\n" ] } ], "prompt_number": 13 }, { "cell_type": "code", "collapsed": false, "input": [ "#option - number of processes \n", "!{bsmap}bsmap -a {wd}{fid}_R1a.fastq -b {wd}{fid}_R2a.fastq -d {genome} -o bsmap_out.sam -p 4 \n", "!python {bsmap}methratio.py -d {genome} -u -z -g -o methratio_out.txt -s {bsmap}samtools bsmap_out.sam \n", "#command for only obtaining the context '__CG_'\n", "!grep \"[A-Z][A-Z]CG[A-Z]\" methratio_out_CG.txt \n", "#5x coverage\n", "!awk '{if ($8 >= 5) print $1,$2-1,$2+1,\"CpG\",$5}' filt_methratio_out_CG.igv \n", "!tr ' ' \"\\t\" filt_methratio_{fid}.igv" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ "\r\n", "BSMAP v2.74\r\n", "Start at: Sun Mar 16 12:08:52 2014\r\n", "\r\n", "Input reference file: /Volumes/web/whale/ensembl/ftp.ensemblgenomes.org/pub/release-21/metazoa/fasta/crassostrea_gigas/dna/Crassostrea_gigas.GCA_000297895.1.21.dna_sm.genome.fa" ] }, { "output_type": "stream", "stream": "stdout", "text": [ " \t(format: FASTA)\r\n" ] }, { "output_type": "stream", "stream": "stdout", "text": [ "Load in 7658 db seqs, total size 557717710 bp. 22 secs passed\r\n", "total_kmers: 43046721\r\n" ] }, { "output_type": "stream", "stream": "stdout", "text": [ "Create seed table. 63 secs passed\r\n", "max number of mismatches: read_length * 8% \tmax gap size: 0\r\n", "kmer cut-off ratio: 5e-07\r\n", "max multi-hits: 100\tmax Ns: 5\tseed size: 16\tindex interval: 4\r\n", "quality cutoff: 0\tbase quality char: '!'\r\n", "min fragment size:28\tmax fragemt size:500\r\n", "start from read #1\tend at read #4294967295\r\n", "additional alignment: T in reads => C in reference\r\n", "mapping strand (read_1): ++,-+\r\n", "mapping strand (read_2): +-,--\r\n", "Pair-end alignment(4 threads)\r\n", "Input read file #1: /Volumes/web/cnidarian/BiGo_larvae_merge/CgM3_R1a.fastq" ] }, { "output_type": "stream", "stream": "stdout", "text": [ " \t(format: FASTQ)\r\n", "Input read file #2: /Volumes/web/cnidarian/BiGo_larvae_merge/CgM3_R2a.fastq \t(format: FASTQ)\r\n", "Output file: bsmap_out.sam\t (format: SAM)\r\n" ] }, { "output_type": "stream", "stream": "stdout", "text": [ "Thread #3: \t200000 read pairs finished. 98 secs passed\r\n" ] }, { "output_type": "stream", "stream": "stdout", "text": [ "Thread #1: \t100000 read pairs finished. 98 secs passed\r\n" ] 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finished. 1388 secs passed\r\n" ] }, { "output_type": "stream", "stream": "stdout", "text": [ "Thread #3: \t7650000 read pairs finished. 1400 secs passed\r\n" ] }, { "output_type": "stream", "stream": "stdout", "text": [ "Thread #1: \t7700000 read pairs finished. 1412 secs passed\r\n" ] }, { "output_type": "stream", "stream": "stdout", "text": [ "Thread #2: \t7750000 read pairs finished. 1414 secs passed\r\n" ] }, { "output_type": "stream", "stream": "stdout", "text": [ "Thread #0: \t7800000 read pairs finished. 1423 secs passed\r\n" ] }, { "output_type": "stream", "stream": "stdout", "text": [ "Thread #3: \t7850000 read pairs finished. 1435 secs passed\r\n" ] }, { "output_type": "stream", "stream": "stdout", "text": [ "Thread #1: \t7900000 read pairs finished. 1448 secs passed\r\n" ] }, { "output_type": "stream", "stream": "stdout", "text": [ "Thread #2: \t7950000 read pairs finished. 1449 secs passed\r\n" ] }, { "output_type": "stream", "stream": "stdout", "text": [ "Thread #0: \t8000000 read pairs finished. 1456 secs passed\r\n" ] }, { "output_type": "stream", "stream": "stdout", "text": [ "Thread #1: \t8078115 read pairs finished. 1461 secs passed\r\n" ] }, { "output_type": "stream", "stream": "stdout", "text": [ "Thread #3: \t8050000 read pairs finished. 1463 secs passed\r\n" ] }, { "output_type": "stream", "stream": "stdout", "text": [ "Total number of aligned reads: \r\n", "pairs: 4380128 (54%)\r\n", "single a: 1426879 (18%)\r\n", "single b: 1168161 (14%)\r\n", "Done.\r\n", "Finished at Sun Mar 16 12:33:15 2014\r\n", "Total time consumed: 1463 secs\r\n" ] }, { "output_type": "stream", "stream": "stdout", "text": [ "@ Sun Mar 16 12:33:17 2014: reading reference /Volumes/web/whale/ensembl/ftp.ensemblgenomes.org/pub/release-21/metazoa/fasta/crassostrea_gigas/dna/Crassostrea_gigas.GCA_000297895.1.21.dna_sm.genome.fa ...\r\n" ] }, { "output_type": "stream", "stream": "stdout", "text": [ "@ Sun Mar 16 12:34:09 2014: reading bsmap_out.sam ...\r\n" ] }, { "output_type": "stream", "stream": "stdout", "text": [ "[samopen] SAM header is present: 7658 sequences.\r\n" ] }, { "output_type": "stream", "stream": "stdout", "text": [ "\t@ Sun Mar 16 12:43:14 2014: read 10000000 lines\r\n" ] }, { "output_type": "stream", "stream": "stdout", "text": [ "@ Sun Mar 16 12:44:27 2014: combining CpG methylation from both strands ...\r\n" ] }, { "output_type": "stream", "stream": "stdout", "text": [ "@ Sun Mar 16 12:45:10 2014: writing methratio_out.txt ...\r\n" ] }, { "output_type": "stream", "stream": "stdout", "text": [ "@ Sun Mar 16 13:01:19 2014: done.\r\n", "total 9597901 valid mappings, 53820491 covered cytosines, average coverage: 1.79 fold.\r\n" ] } ], "prompt_number": 14 }, { "cell_type": "code", "collapsed": false, "input": [ "\n", "#file ID \n", "fid=\"CgT1D3\"\n", "\n", "#TIMESTAMP\n", "date=!date +%m%d_%H%M\n", "\n", "#working directory (parent)\n", "wd=\"/Volumes/web/cnidarian/BiGo_larvae_merge/\"" ], "language": "python", "metadata": {}, "outputs": [], "prompt_number": 15 }, { "cell_type": "code", "collapsed": false, "input": [ "cd {wd}" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ "/Volumes/web/cnidarian/BiGo_larvae_merge\n" ] } ], "prompt_number": 16 }, { "cell_type": "code", "collapsed": false, "input": [ "mkdir {fid}_{date}" ], "language": "python", "metadata": {}, "outputs": [], "prompt_number": 17 }, { "cell_type": "code", "collapsed": false, "input": [ "cd {fid}_{date}" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ "/Volumes/web/cnidarian/BiGo_larvae_merge/CgT1D3_[0316_1306]\n" ] } ], "prompt_number": 18 }, { "cell_type": "code", "collapsed": false, "input": [ "#option - number of processes \n", "!{bsmap}bsmap -a {wd}{fid}_R1a.fastq -b {wd}{fid}_R2a.fastq -d {genome} -o bsmap_out.sam -p 4 \n", "!python {bsmap}methratio.py -d {genome} -u -z -g -o methratio_out.txt -s {bsmap}samtools bsmap_out.sam \n", "#command for only obtaining the context '__CG_'\n", "!grep \"[A-Z][A-Z]CG[A-Z]\" methratio_out_CG.txt \n", "#5x coverage\n", "!awk '{if ($8 >= 5) print $1,$2-1,$2+1,\"CpG\",$5}' filt_methratio_out_CG.igv \n", "!tr ' ' \"\\t\" filt_methratio_{fid}.igv" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ "\r\n", "BSMAP v2.74\r\n", "Start at: Sun Mar 16 13:06:42 2014\r\n", "\r\n", "Input reference file: /Volumes/web/whale/ensembl/ftp.ensemblgenomes.org/pub/release-21/metazoa/fasta/crassostrea_gigas/dna/Crassostrea_gigas.GCA_000297895.1.21.dna_sm.genome.fa" ] }, { "output_type": "stream", "stream": "stdout", "text": [ " \t(format: FASTA)\r\n" ] }, { "output_type": "stream", "stream": "stdout", "text": [ "Load in 7658 db seqs, total size 557717710 bp. 22 secs passed\r\n", "total_kmers: 43046721\r\n" ] }, { "output_type": "stream", "stream": "stdout", "text": [ "Create seed table. 63 secs passed\r\n", "max number of mismatches: read_length * 8% \tmax gap size: 0\r\n", "kmer cut-off ratio: 5e-07\r\n", "max multi-hits: 100\tmax Ns: 5\tseed size: 16\tindex interval: 4\r\n", "quality cutoff: 0\tbase quality char: '!'\r\n", "min fragment size:28\tmax fragemt size:500\r\n", "start from read #1\tend at read #4294967295\r\n", "additional alignment: T in reads => C in reference\r\n", "mapping strand (read_1): ++,-+\r\n", "mapping strand (read_2): +-,--\r\n", "Pair-end alignment(4 threads)\r\n", "Input read file #1: /Volumes/web/cnidarian/BiGo_larvae_merge/CgT1D3_R1a.fastq" ] }, { "output_type": "stream", "stream": "stdout", "text": [ " \t(format: FASTQ)\r\n", "Input read file #2: /Volumes/web/cnidarian/BiGo_larvae_merge/CgT1D3_R2a.fastq \t(format: FASTQ)\r\n", "Output file: bsmap_out.sam\t (format: SAM)\r\n" ] }, { "output_type": "stream", "stream": "stdout", "text": [ "Thread #1: \t100000 read pairs finished. 101 secs passed\r\n" ] }, { "output_type": "stream", "stream": "stdout", "text": [ "Thread #0: 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read pairs finished. 1036 secs passed\r\n" ] }, { "output_type": "stream", "stream": "stdout", "text": [ "Thread #0: \t5300000 read pairs finished. 1040 secs passed\r\n" ] }, { "output_type": "stream", "stream": "stdout", "text": [ "Thread #3: \t5350000 read pairs finished. 1046 secs passed\r\n" ] }, { "output_type": "stream", "stream": "stdout", "text": [ "Thread #2: \t5400000 read pairs finished. 1050 secs passed\r\n" ] }, { "output_type": "stream", "stream": "stdout", "text": [ "Thread #0: \t5465974 read pairs finished. 1050 secs passed\r\n" ] }, { "output_type": "stream", "stream": "stdout", "text": [ "Thread #1: \t5450000 read pairs finished. 1061 secs passed\r\n" ] }, { "output_type": "stream", "stream": "stdout", "text": [ "Total number of aligned reads: \r\n", "pairs: 2625402 (48%)\r\n", "single a: 1124227 (21%)\r\n", "single b: 885757 (16%)\r\n", "Done.\r\n", "Finished at Sun Mar 16 13:24:24 2014\r\n", "Total time consumed: 1062 secs\r\n" ] }, { "output_type": "stream", "stream": "stdout", "text": [ "@ Sun Mar 16 13:24:25 2014: reading reference /Volumes/web/whale/ensembl/ftp.ensemblgenomes.org/pub/release-21/metazoa/fasta/crassostrea_gigas/dna/Crassostrea_gigas.GCA_000297895.1.21.dna_sm.genome.fa ...\r\n" ] }, { "output_type": "stream", "stream": "stdout", "text": [ "@ Sun Mar 16 13:25:16 2014: reading bsmap_out.sam ...\r\n" ] }, { "output_type": "stream", "stream": "stdout", "text": [ "[samopen] SAM header is present: 7658 sequences.\r\n" ] }, { "output_type": "stream", "stream": "stdout", "text": [ "@ Sun Mar 16 13:30:53 2014: combining CpG methylation from both strands ...\r\n" ] }, { "output_type": "stream", "stream": "stdout", "text": [ "@ Sun Mar 16 13:31:31 2014: writing methratio_out.txt ...\r\n" ] }, { "output_type": "stream", "stream": "stdout", "text": [ "@ Sun Mar 16 13:44:03 2014: done.\r\n", "total 5964269 valid mappings, 39695564 covered cytosines, average coverage: 1.51 fold.\r\n" ] } ], "prompt_number": 19 }, { "cell_type": "code", "collapsed": false, "input": [ "#file ID\n", "fid=\"CgT1D5\"\n", "\n", "#TIMESTAMP\n", "date=!date +%m%d_%H%M\n", "\n", "#working directory (parent)\n", "wd=\"/Volumes/web/cnidarian/BiGo_larvae_merge/\"\n" ], "language": "python", "metadata": {}, "outputs": [], "prompt_number": 20 }, { "cell_type": "code", "collapsed": false, "input": [ "cd {wd}" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ "/Volumes/web/cnidarian/BiGo_larvae_merge\n" ] } ], "prompt_number": 21 }, { "cell_type": "code", "collapsed": false, "input": [ "mkdir {fid}_{date}" ], "language": "python", "metadata": {}, "outputs": [], "prompt_number": 22 }, { "cell_type": "code", "collapsed": false, "input": [ "cd {fid}_{date}" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ "/Volumes/web/cnidarian/BiGo_larvae_merge/CgT1D5_[0316_1346]\n" ] } ], "prompt_number": 23 }, { "cell_type": "code", "collapsed": false, "input": [ "#option - number of processes \n", "!{bsmap}bsmap -a {wd}{fid}_R1a.fastq -b {wd}{fid}_R2a.fastq -d {genome} -o bsmap_out.sam -p 4 \n", "!python {bsmap}methratio.py -d {genome} -u -z -g -o methratio_out.txt -s {bsmap}samtools bsmap_out.sam \n", "#command for only obtaining the context '__CG_'\n", "!grep \"[A-Z][A-Z]CG[A-Z]\" methratio_out_CG.txt \n", "#5x coverage\n", "!awk '{if ($8 >= 5) print $1,$2-1,$2+1,\"CpG\",$5}' filt_methratio_out_CG.igv \n", "!tr ' ' \"\\t\" filt_methratio_{fid}.igv" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ "\r\n", "BSMAP v2.74\r\n", "Start at: Sun Mar 16 13:46:58 2014\r\n", "\r\n", "Input reference file: /Volumes/web/whale/ensembl/ftp.ensemblgenomes.org/pub/release-21/metazoa/fasta/crassostrea_gigas/dna/Crassostrea_gigas.GCA_000297895.1.21.dna_sm.genome.fa" ] }, { "output_type": "stream", "stream": "stdout", "text": [ " \t(format: FASTA)\r\n" ] }, { "output_type": "stream", "stream": "stdout", "text": [ "Load in 7658 db seqs, total size 557717710 bp. 22 secs passed\r\n", "total_kmers: 43046721\r\n" ] }, { "output_type": "stream", "stream": "stdout", "text": [ "Create seed table. 68 secs passed\r\n", "max number of mismatches: read_length * 8% \tmax gap size: 0\r\n", "kmer cut-off ratio: 5e-07\r\n", "max multi-hits: 100\tmax Ns: 5\tseed size: 16\tindex interval: 4\r\n", "quality cutoff: 0\tbase quality char: '!'\r\n", "min fragment size:28\tmax fragemt size:500\r\n", "start from read #1\tend at read #4294967295\r\n", "additional alignment: T in reads => C in reference\r\n", "mapping strand (read_1): ++,-+\r\n", "mapping strand (read_2): +-,--\r\n", "Pair-end alignment(4 threads)\r\n", "Input read file #1: /Volumes/web/cnidarian/BiGo_larvae_merge/CgT1D5_R1a.fastq" ] }, { "output_type": "stream", "stream": "stdout", "text": [ " \t(format: FASTQ)\r\n", "Input read file #2: /Volumes/web/cnidarian/BiGo_larvae_merge/CgT1D5_R2a.fastq 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"text": [ "Thread #2: \t6250000 read pairs finished. 1413 secs passed\r\n" ] }, { "output_type": "stream", "stream": "stdout", "text": [ "Thread #3: \t6300000 read pairs finished. 1417 secs passed\r\n" ] }, { "output_type": "stream", "stream": "stdout", "text": [ "Total number of aligned reads: \r\n", "pairs: 2608088 (41%)\r\n", "single a: 1736286 (27%)\r\n", "single b: 1343344 (21%)\r\n", "Done.\r\n", "Finished at Sun Mar 16 14:10:36 2014\r\n", "Total time consumed: 1418 secs\r\n" ] }, { "output_type": "stream", "stream": "stdout", "text": [ "@ Sun Mar 16 14:10:37 2014: reading reference /Volumes/web/whale/ensembl/ftp.ensemblgenomes.org/pub/release-21/metazoa/fasta/crassostrea_gigas/dna/Crassostrea_gigas.GCA_000297895.1.21.dna_sm.genome.fa ...\r\n" ] }, { "output_type": "stream", "stream": "stdout", "text": [ "@ Sun Mar 16 14:11:29 2014: reading bsmap_out.sam ...\r\n" ] }, { "output_type": "stream", "stream": "stdout", "text": [ "[samopen] SAM header is present: 7658 sequences.\r\n" ] }, { "output_type": "stream", "stream": "stdout", "text": [ "@ Sun Mar 16 14:18:41 2014: combining CpG methylation from both strands ...\r\n" ] }, { "output_type": "stream", "stream": "stdout", "text": [ "@ Sun Mar 16 14:19:18 2014: writing methratio_out.txt ...\r\n" ] }, { "output_type": "stream", "stream": "stdout", "text": [ "@ Sun Mar 16 14:33:02 2014: done.\r\n", "total 6801985 valid mappings, 45492773 covered cytosines, average coverage: 1.54 fold.\r\n" ] } ], "prompt_number": 24 }, { "cell_type": "code", "collapsed": false, "input": [ "#file ID\n", "fid=\"CgT3D3\"\n", "\n", "#TIMESTAMP\n", "date=!date +%m%d_%H%M\n", "\n", "#working directory (parent)\n", "wd=\"/Volumes/web/cnidarian/BiGo_larvae_merge/\"\n" ], "language": "python", "metadata": {}, "outputs": [], "prompt_number": 25 }, { "cell_type": "code", "collapsed": false, "input": [ "cd {wd}" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ "/Volumes/web/cnidarian/BiGo_larvae_merge\n" ] } ], "prompt_number": 26 }, { "cell_type": "code", "collapsed": false, "input": [ "mkdir {fid}_{date}" ], "language": "python", "metadata": {}, "outputs": [], "prompt_number": 27 }, { "cell_type": "code", "collapsed": false, "input": [ "cd {fid}_{date}" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ "/Volumes/web/cnidarian/BiGo_larvae_merge/CgT3D3_[0316_1436]\n" ] } ], "prompt_number": 28 }, { "cell_type": "code", "collapsed": false, "input": [ "#option - number of processes \n", "!{bsmap}bsmap -a {wd}{fid}_R1a.fastq -b {wd}{fid}_R2a.fastq -d {genome} -o bsmap_out.sam -p 4 \n", "!python {bsmap}methratio.py -d {genome} -u -z -g -o methratio_out.txt -s {bsmap}samtools bsmap_out.sam \n", "#command for only obtaining the context '__CG_'\n", "!grep \"[A-Z][A-Z]CG[A-Z]\" methratio_out_CG.txt \n", "#5x coverage\n", "!awk '{if ($8 >= 5) print $1,$2-1,$2+1,\"CpG\",$5}' filt_methratio_out_CG.igv \n", "!tr ' ' \"\\t\" filt_methratio_{fid}.igv" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ "\r\n", "BSMAP v2.74\r\n", "Start at: Sun Mar 16 14:36:38 2014\r\n", "\r\n", "Input reference file: /Volumes/web/whale/ensembl/ftp.ensemblgenomes.org/pub/release-21/metazoa/fasta/crassostrea_gigas/dna/Crassostrea_gigas.GCA_000297895.1.21.dna_sm.genome.fa" ] }, { "output_type": "stream", "stream": "stdout", "text": [ " \t(format: FASTA)\r\n" ] }, { "output_type": "stream", "stream": "stdout", "text": [ "Load in 7658 db seqs, total size 557717710 bp. 22 secs passed\r\n", "total_kmers: 43046721\r\n" ] }, { "output_type": "stream", "stream": "stdout", "text": [ "Create seed table. 63 secs passed\r\n", "max number of mismatches: read_length * 8% \tmax gap size: 0\r\n", "kmer cut-off ratio: 5e-07\r\n", "max multi-hits: 100\tmax Ns: 5\tseed size: 16\tindex interval: 4\r\n", "quality cutoff: 0\tbase quality char: '!'\r\n", "min fragment size:28\tmax fragemt size:500\r\n", "start from read #1\tend at read #4294967295\r\n", "additional alignment: T in reads => C in reference\r\n", "mapping strand (read_1): ++,-+\r\n", "mapping strand (read_2): +-,--\r\n", "Pair-end alignment(4 threads)\r\n", "Input read file #1: /Volumes/web/cnidarian/BiGo_larvae_merge/CgT3D3_R1a.fastq \t(format: FASTQ)\r\n", "Input read file #2: /Volumes/web/cnidarian/BiGo_larvae_merge/CgT3D3_R2a.fastq" ] }, { "output_type": "stream", "stream": "stdout", "text": [ " \t(format: FASTQ)\r\n", "Output file: bsmap_out.sam\t (format: SAM)\r\n" ] }, { "output_type": "stream", "stream": "stdout", "text": [ "Thread #2: \t150000 read pairs finished. 100 secs passed\r\n" ] }, { "output_type": "stream", "stream": "stdout", "text": [ "Thread #3: \t50000 read pairs finished. 100 secs passed\r\n" ] }, { "output_type": "stream", "stream": "stdout", "text": [ "Thread #1: \t100000 read pairs finished. 101 secs passed\r\n" ] }, { 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"stream": "stdout", "text": [ "Thread #0: \t7380649 read pairs finished. 1414 secs passed\r\n" ] }, { "output_type": "stream", "stream": "stdout", "text": [ "Thread #2: \t7300000 read pairs finished. 1415 secs passed\r\n" ] }, { "output_type": "stream", "stream": "stdout", "text": [ "Thread #1: \t7350000 read pairs finished. 1421 secs passed\r\n" ] }, { "output_type": "stream", "stream": "stdout", "text": [ "Total number of aligned reads: \r\n", "pairs: 3906464 (53%)\r\n", "single a: 1418844 (19%)\r\n", "single b: 1116765 (15%)\r\n", "Done.\r\n", "Finished at Sun Mar 16 15:00:20 2014\r\n", "Total time consumed: 1422 secs\r\n" ] }, { "output_type": "stream", "stream": "stdout", "text": [ "@ Sun Mar 16 15:00:22 2014: reading reference /Volumes/web/whale/ensembl/ftp.ensemblgenomes.org/pub/release-21/metazoa/fasta/crassostrea_gigas/dna/Crassostrea_gigas.GCA_000297895.1.21.dna_sm.genome.fa ...\r\n" ] }, { "output_type": "stream", "stream": "stdout", "text": [ "@ Sun Mar 16 15:01:23 2014: reading bsmap_out.sam ...\r\n" ] }, { "output_type": "stream", "stream": "stdout", "text": [ "[samopen] SAM header is present: 7658 sequences.\r\n" ] }, { "output_type": "stream", "stream": "stdout", "text": [ "\t@ Sun Mar 16 15:10:55 2014: read 10000000 lines\r\n" ] }, { "output_type": "stream", "stream": "stdout", "text": [ "@ Sun Mar 16 15:11:15 2014: combining CpG methylation from both strands ...\r\n" ] }, { "output_type": "stream", "stream": "stdout", "text": [ "@ Sun Mar 16 15:12:07 2014: writing methratio_out.txt ...\r\n" ] }, { "output_type": "stream", "stream": "stdout", "text": [ "@ Sun Mar 16 15:28:02 2014: done.\r\n", "total 8688793 valid mappings, 52876971 covered cytosines, average coverage: 1.67 fold.\r\n" ] } ], "prompt_number": 29 }, { "cell_type": "code", "collapsed": false, "input": [ "#file ID\n", "fid=\"CgT3D5\"\n", "\n", "#TIMESTAMP\n", "date=!date +%m%d_%H%M\n", "\n", "#working directory (parent)\n", "wd=\"/Volumes/web/cnidarian/BiGo_larvae_merge/\"\n" ], "language": "python", "metadata": {}, "outputs": [], "prompt_number": 30 }, { "cell_type": "code", "collapsed": false, "input": [ "cd {wd}" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ "/Volumes/web/cnidarian/BiGo_larvae_merge\n" ] } ], "prompt_number": 31 }, { "cell_type": "code", "collapsed": false, "input": [ "mkdir {fid}_{date}" ], "language": "python", "metadata": {}, "outputs": [], "prompt_number": 32 }, { "cell_type": "code", "collapsed": false, "input": [ "cd {fid}_{date}" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ "/Volumes/web/cnidarian/BiGo_larvae_merge/CgT3D5_[0316_1532]\n" ] } ], "prompt_number": 33 }, { "cell_type": "code", "collapsed": false, "input": [ "#option - number of processes \n", "!{bsmap}bsmap -a {wd}{fid}_R1a.fastq -b {wd}{fid}_R2a.fastq -d {genome} -o bsmap_out.sam -p 4 \n", "!python {bsmap}methratio.py -d {genome} -u -z -g -o methratio_out.txt -s {bsmap}samtools bsmap_out.sam \n", "#command for only obtaining the context '__CG_'\n", "!grep \"[A-Z][A-Z]CG[A-Z]\" methratio_out_CG.txt \n", "#5x coverage\n", "!awk '{if ($8 >= 5) print $1,$2-1,$2+1,\"CpG\",$5}' filt_methratio_out_CG.igv \n", "!tr ' ' \"\\t\" filt_methratio_{fid}.igv" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ "\r\n", "BSMAP v2.74\r\n", "Start at: Sun Mar 16 15:32:31 2014\r\n", "\r\n", "Input reference file: /Volumes/web/whale/ensembl/ftp.ensemblgenomes.org/pub/release-21/metazoa/fasta/crassostrea_gigas/dna/Crassostrea_gigas.GCA_000297895.1.21.dna_sm.genome.fa" ] }, { "output_type": "stream", "stream": "stdout", "text": [ " \t(format: FASTA)\r\n" ] }, { "output_type": "stream", "stream": "stdout", "text": [ "Load in 7658 db seqs, total size 557717710 bp. 22 secs passed\r\n", "total_kmers: 43046721\r\n" ] }, { "output_type": "stream", "stream": "stdout", "text": [ "Create seed table. 74 secs passed\r\n", "max number of mismatches: read_length * 8% \tmax gap size: 0\r\n", "kmer cut-off ratio: 5e-07\r\n", "max multi-hits: 100\tmax Ns: 5\tseed size: 16\tindex interval: 4\r\n", "quality cutoff: 0\tbase quality char: '!'\r\n", "min fragment size:28\tmax fragemt size:500\r\n", "start from read #1\tend at read #4294967295\r\n", "additional alignment: T in reads => C in reference\r\n", "mapping strand (read_1): ++,-+\r\n", "mapping strand (read_2): +-,--\r\n", "Pair-end alignment(4 threads)\r\n", "Input read file #1: /Volumes/web/cnidarian/BiGo_larvae_merge/CgT3D5_R1a.fastq \t(format: FASTQ)\r\n", "Input read file #2: /Volumes/web/cnidarian/BiGo_larvae_merge/CgT3D5_R2a.fastq" ] }, { "output_type": "stream", "stream": "stdout", "text": [ " \t(format: FASTQ)\r\n", "Output file: bsmap_out.sam\t (format: SAM)\r\n" ] }, { "output_type": "stream", "stream": "stdout", "text": [ "Thread #2: \t150000 read pairs finished. 130 secs passed\r\n" ] }, { "output_type": "stream", 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passed\r\n" ] }, { "output_type": "stream", "stream": "stdout", "text": [ "Thread #3: \t6400000 read pairs finished. 1964 secs passed\r\n" ] }, { "output_type": "stream", "stream": "stdout", "text": [ "Thread #2: \t6450000 read pairs finished. 1993 secs passed\r\n" ] }, { "output_type": "stream", "stream": "stdout", "text": [ "Thread #0: \t6500000 read pairs finished. 2013 secs passed\r\n" ] }, { "output_type": "stream", "stream": "stdout", "text": [ "Thread #1: \t6550000 read pairs finished. 2015 secs passed\r\n" ] }, { "output_type": "stream", "stream": "stdout", "text": [ "Thread #3: \t6600000 read pairs finished. 2020 secs passed\r\n" ] }, { "output_type": "stream", "stream": "stdout", "text": [ "Thread #2: \t6650000 read pairs finished. 2047 secs passed\r\n" ] }, { "output_type": "stream", "stream": "stdout", "text": [ "Thread #0: \t6700000 read pairs finished. 2066 secs passed\r\n" ] }, { "output_type": "stream", "stream": "stdout", "text": [ "Thread #1: \t6750000 read pairs finished. 2068 secs passed\r\n" ] }, { "output_type": "stream", "stream": "stdout", "text": [ "Thread #3: \t6800000 read pairs finished. 2076 secs passed\r\n" ] }, { "output_type": "stream", "stream": "stdout", "text": [ "Thread #2: \t6850000 read pairs finished. 2096 secs passed\r\n" ] }, { "output_type": "stream", "stream": "stdout", "text": [ "Thread #0: \t6900000 read pairs finished. 2113 secs passed\r\n" ] }, { "output_type": "stream", "stream": "stdout", "text": [ "Thread #1: \t6950000 read pairs finished. 2114 secs passed\r\n" ] }, { "output_type": "stream", "stream": "stdout", "text": [ "Thread #3: \t7000000 read pairs finished. 2120 secs passed\r\n" ] }, { "output_type": "stream", "stream": "stdout", "text": [ "Thread #2: \t7050000 read pairs finished. 2136 secs passed\r\n" ] }, { "output_type": "stream", "stream": "stdout", "text": [ "Thread #0: \t7100000 read pairs finished. 2149 secs passed\r\n" ] }, { "output_type": "stream", "stream": "stdout", "text": [ "Thread #1: \t7150000 read pairs finished. 2151 secs passed\r\n" ] }, { "output_type": "stream", "stream": "stdout", "text": [ "Thread #3: \t7200000 read pairs finished. 2155 secs passed\r\n" ] }, { "output_type": "stream", "stream": "stdout", "text": [ "Thread #3: \t7350645 read pairs finished. 2156 secs passed\r\n" ] }, { "output_type": "stream", "stream": "stdout", "text": [ "Thread #2: \t7250000 read pairs finished. 2169 secs passed\r\n" ] }, { "output_type": "stream", "stream": "stdout", "text": [ "Thread #0: \t7300000 read pairs finished. 2177 secs passed\r\n" ] }, { "output_type": "stream", "stream": "stdout", "text": [ "Thread #1: \t7350000 read pairs finished. 2178 secs passed\r\n" ] }, { "output_type": "stream", "stream": "stdout", "text": [ "Total number of aligned reads: \r\n", "pairs: 3946673 (54%)\r\n", "single a: 1329262 (18%)\r\n", "single b: 1076148 (15%)\r\n", "Done.\r\n" ] }, { "output_type": "stream", "stream": "stdout", "text": [ "Finished at Sun Mar 16 16:08:49 2014\r\n", "Total time consumed: 2178 secs\r\n" ] }, { "output_type": "stream", "stream": "stdout", "text": [ "@ Sun Mar 16 16:08:50 2014: reading reference /Volumes/web/whale/ensembl/ftp.ensemblgenomes.org/pub/release-21/metazoa/fasta/crassostrea_gigas/dna/Crassostrea_gigas.GCA_000297895.1.21.dna_sm.genome.fa ...\r\n" ] }, { "output_type": "stream", "stream": "stdout", "text": [ "@ Sun Mar 16 16:09:51 2014: reading bsmap_out.sam ...\r\n" ] }, { "output_type": "stream", "stream": "stdout", "text": [ "[samopen] SAM header is present: 7658 sequences.\r\n" ] }, { "output_type": "stream", "stream": "stdout", "text": [ "\t@ Sun Mar 16 16:19:00 2014: read 10000000 lines\r\n" ] }, { "output_type": "stream", "stream": "stdout", "text": [ "@ Sun Mar 16 16:19:17 2014: combining CpG methylation from both strands ...\r\n" ] }, { "output_type": "stream", "stream": "stdout", "text": [ "@ Sun Mar 16 16:19:59 2014: writing methratio_out.txt ...\r\n" ] }, { "output_type": "stream", "stream": "stdout", "text": [ "@ Sun Mar 16 16:35:26 2014: done.\r\n", "total 8650035 valid mappings, 52138971 covered cytosines, average coverage: 1.70 fold.\r\n" ] } ], "prompt_number": 34 }, { "cell_type": "code", "collapsed": false, "input": [ "!head filt_methratio_{fid}.igv" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ "C13220\t109\t111\tCpG\t0.000\r\n", "C13220\t163\t165\tCpG\t0.000\r\n", "C13490\t82\t84\tCpG\t0.000\r\n", "C13546\t83\t85\tCpG\t0.000\r\n", "C14220\t95\t97\tCpG\t0.000\r\n", "C14450\t59\t61\tCpG\t0.000\r\n", "C14450\t93\t95\tCpG\t0.000\r\n", "C14450\t105\t107\tCpG\t0.000\r\n", "C14450\t117\t119\tCpG\t0.000\r\n", "C14450\t186\t188\tCpG\t0.000\r\n" ] } ], "prompt_number": 35 }, { "cell_type": "heading", "level": 1, "metadata": {}, "source": [ "Comparing two sperm samples" ] }, { "cell_type": "code", "collapsed": false, "input": [ "!head /Volumes/web/cnidarian/BiGo_larvae_merge/CgM1_[0316_0954]/filt_methratio_CgM1.igv" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ "C12768\t102\t104\tCpG\t0.167\r\n", "C12806\t141\t143\tCpG\t0.333\r\n", "C12924\t29\t31\tCpG\t0.000\r\n", "C12924\t37\t39\tCpG\t0.000\r\n", "C12924\t51\t53\tCpG\t0.000\r\n", "C12924\t59\t61\tCpG\t0.000\r\n", "C12924\t126\t128\tCpG\t0.000\r\n", "C12924\t135\t137\tCpG\t0.000\r\n", "C13128\t86\t88\tCpG\t0.000\r\n", "C13208\t82\t84\tCpG\t0.400\r\n" ] } ], "prompt_number": 1 }, { "cell_type": "code", "collapsed": false, "input": [ "!awk '{print ($1\"_\"$2),$1,$2,$3,$4,$5}' \\\n", "/Volumes/web/cnidarian/BiGo_larvae_merge/CgM1_[0316_0954]/filt_methratio_CgM1_id.tab" ], "language": "python", "metadata": {}, "outputs": [], "prompt_number": 10 }, { "cell_type": "code", "collapsed": false, "input": [ "!head /Volumes/web/cnidarian/BiGo_larvae_merge/CgM1_[0316_0954]/filt_methratio_CgM1_id.tab" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ "C12768_102 C12768 102 104 CpG 0.167\r\n", "C12806_141 C12806 141 143 CpG 0.333\r\n", "C12924_29 C12924 29 31 CpG 0.000\r\n", "C12924_37 C12924 37 39 CpG 0.000\r\n", "C12924_51 C12924 51 53 CpG 0.000\r\n", "C12924_59 C12924 59 61 CpG 0.000\r\n", "C12924_126 C12924 126 128 CpG 0.000\r\n", "C12924_135 C12924 135 137 CpG 0.000\r\n", "C13128_86 C13128 86 88 CpG 0.000\r\n", "C13208_82 C13208 82 84 CpG 0.400\r\n" ] } ], "prompt_number": 11 }, { "cell_type": "code", "collapsed": false, "input": [ "!python {spd}singleupload.py -d filt_methratio_CgM1 /Volumes/web/cnidarian/BiGo_larvae_merge/CgM1_[0316_0954]/filt_methratio_CgM1.igv" ], "language": "python", "metadata": {}, "outputs": [] }, { "cell_type": "code", "collapsed": false, "input": [ "!head /Volumes/web/cnidarian/BiGo_larvae_merge/CgM3_[0316_1207]/filt_methratio_CgM3.igv" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ "C13128\t86\t88\tCpG\t0.000\r\n", "C13208\t82\t84\tCpG\t0.429\r\n", "C13442\t64\t66\tCpG\t0.000\r\n", "C13442\t78\t80\tCpG\t0.000\r\n", "C13612\t88\t90\tCpG\t0.000\r\n", "C13992\t53\t55\tCpG\t0.000\r\n", "C14180\t157\t159\tCpG\t0.000\r\n", "C14180\t192\t194\tCpG\t0.000\r\n", "C14220\t95\t97\tCpG\t0.000\r\n", "C14220\t142\t144\tCpG\t0.000\r\n" ] } ], "prompt_number": 2 }, { "cell_type": "heading", "level": 3, "metadata": {}, "source": [ "Try SQLShare " ] }, { "cell_type": "code", "collapsed": false, "input": [ "#Location of SQLShare python tools: you can empty (\"\") if tools are in PATH\n", "spd=\"/Users/sr320/sqlshare-pythonclient/tools/\"" ], "language": "python", "metadata": {}, "outputs": [], "prompt_number": 3 }, { "cell_type": "code", "collapsed": false, "input": [ "!python {spd}singleupload.py -d filt_methratio_CgM1 /Volumes/web/cnidarian/BiGo_larvae_merge/CgM1_[0316_0954]/filt_methratio_CgM1.igv" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ "processing chunk line 0 to 380223 (18.4622421265 s elapsed)\r\n", "pushing /Volumes/web/cnidarian/BiGo_larvae_merge/CgM1_[0316_0954]/filt_methratio_CgM1.igv...\r\n" ] }, { "output_type": "stream", "stream": "stdout", "text": [ "parsing D588E61B...\r\n" ] }, { "output_type": "stream", "stream": "stdout", "text": [ "finished filt_methratio_CgM1\r\n" ] } ], "prompt_number": 4 }, { "cell_type": "code", "collapsed": false, "input": [ "!python {spd}singleupload.py -d filt_methratio_CgM3 /Volumes/web/cnidarian/BiGo_larvae_merge/CgM3_[0316_1207]/filt_methratio_CgM3.igv" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ "processing chunk line 0 to 404025 (15.2012460232 s elapsed)\r\n", "pushing /Volumes/web/cnidarian/BiGo_larvae_merge/CgM3_[0316_1207]/filt_methratio_CgM3.igv...\r\n" ] }, { "output_type": "stream", "stream": "stdout", "text": [ "parsing A7780515...\r\n" ] }, { "output_type": "stream", "stream": "stdout", "text": [ "finished filt_methratio_CgM3\r\n" ] } ], "prompt_number": 5 }, { "cell_type": "heading", "level": 1, "metadata": {}, "source": [ "Coverting files for Methylkit" ] }, { "cell_type": "code", "collapsed": false, "input": [ "target" ], "language": "python", "metadata": {}, "outputs": [] }, { "cell_type": "markdown", "metadata": {}, "source": [ "\"methylkit_-_R_package_for_DNA_methylation_analysis_-_Google_Project_Hosting_18E63628.png\"/" ] }, { "cell_type": "raw", "metadata": {}, "source": [ "!head -2 /Volumes/web/cnidarian/BiGo_larvae_merge/CgM1_[0316_0954]/methratio_out_CG.txt" ] }, { "cell_type": "code", "collapsed": false, "input": [ "cat /Volumes/web/Mollusk/bs_larvae_exp/methratio.awk.sh" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ "#!/usr/bin/awk -f\r\n", "\r\n", "BEGIN{ print \"chr.Base\\tchr\\tbase\\tstrand\\tcoverage\\tfreqC\\tfreqT\" }\r\n", "{\r\n", "\tif ($3 == \"+\") {\r\n", "\t\tstrand=\"F\"\r\n", " \t} else {\r\n", "\t\tstrand=\"R\"\r\n", "\t}\r\n", "\r\n", "\tFC=$7/$8\r\n", "\tFT=1-FC\r\n", "\tchrbase=$1\".\"$2\r\n", "\tprintf \"%s\\t%s\\t%s\\t%s\\t%d\\t%.2f\\t%.2f\\n\",\r\n", "\t\tchrbase, $1, $2, strand, $8, FC, FT\r\n", "}\r\n" ] } ], "prompt_number": 7 }, { "cell_type": "raw", "metadata": {}, "source": [ "!/Volumes/web/Mollusk/bs_larvae_exp/methratio.awk.sh \\\n", "/Volumes/web/cnidarian/BiGo_larvae_merge/CgM1_[0316_0954]/methratio_out_CG.txt > \\\n", "/Volumes/web/cnidarian/CgM1_[0316_0954]mk.txt" ] }, { "cell_type": "code", "collapsed": false, "input": [ "!head /Volumes/web/cnidarian/CgM1_[0316_0954]mk.txt" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ "chr.Base\tchr\tbase\tstrand\tcoverage\tfreqC\tfreqT\r\n", "C12706.69\tC12706\t69\tF\t1\t0.00\t1.00\r\n", "C12706.71\tC12706\t71\tF\t1\t0.00\t1.00\r\n", "C12722.104\tC12722\t104\tF\t2\t0.50\t0.50\r\n", "C12722.134\tC12722\t134\tF\t2\t0.50\t0.50\r\n", "C12768.103\tC12768\t103\tF\t6\t0.17\t0.83\r\n", "C12768.119\tC12768\t119\tF\t4\t0.25\t0.75\r\n", "C12768.145\tC12768\t145\tF\t3\t0.00\t1.00\r\n", "C12768.161\tC12768\t161\tF\t1\t0.00\t1.00\r\n", "C12778.114\tC12778\t114\tF\t1\t0.00\t1.00\r\n" ] } ], "prompt_number": 9 }, { "cell_type": "heading", "level": 2, "metadata": {}, "source": [ "List of methratio files" ] }, { "cell_type": "raw", "metadata": {}, "source": [ "/Volumes/web/cnidarian/BiGo_larvae_merge/CgM1_[0316_0954]/\n", "/Volumes/web/cnidarian/BiGo_larvae_merge/CgM3_[0316_1207]/\n", "/Volumes/web/cnidarian/BiGo_larvae_merge/CgT1D3_[0316_1306]/\n", "/Volumes/web/cnidarian/BiGo_larvae_merge/CgT1D5_[0316_1346]/\n", "/Volumes/web/cnidarian/BiGo_larvae_merge/CgT3D3_[0316_1436]/\n", "/Volumes/web/cnidarian/BiGo_larvae_merge/CgT3D5_[0316_1532]/\n", "\n" ] }, { "cell_type": "code", "collapsed": false, "input": [ "!head -2 /Volumes/web/cnidarian/BiGo_larvae_merge/CgM1_[0316_0954]/methratio_out.txt\n" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ "chr\tpos\tstrand\tcontext\tratio\teff_CT_count\tC_count\tCT_count\trev_G_count\trev_GA_count\tCI_lower\tCI_upper\r\n", "C12706\t51\t-\tCAGAG\t0.000\t1.00\t0\t1\t0\t0\t0.000\t0.793\r\n" ] } ], "prompt_number": 11 }, { "cell_type": "code", "collapsed": false, "input": [ "cd /Volumes/web/cnidarian/BiGo_larvae_merge/CgM1_[0316_0954]/" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ "/Volumes/web/cnidarian/BiGo_larvae_merge/CgM1_[0316_0954]\n" ] } ], "prompt_number": 26 }, { "cell_type": "code", "collapsed": false, "input": [ "!grep \"[A-Z][A-Z]CG[A-Z]\" mk_methratio_out_CG.txt \n" ], "language": "python", "metadata": {}, "outputs": [], "prompt_number": 2 }, { "cell_type": "code", "collapsed": false, "input": [ "!awk '{if ($8 >= 5) print $1,$2,$2+1,$3,$8,($7/$8),(1-($7/$8))}' mk_methratio_out_CG5x.txt " ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ "awk: division by zero\r\n", " input record number 1, file \r\n", " source line number 1\r\n" ] } ], "prompt_number": 34 }, { "cell_type": "code", "collapsed": false, "input": [ "!head mk_methratio_out_CG5x.txt " ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ "C12706\t69\t+\tTCCGC\t0.000\t1.00\t0\t1\t1\t1\t0.000\t0.793\r\n", "C12706\t71\t+\tCGCGT\t0.000\t1.00\t0\t1\t1\t1\t0.000\t0.793\r\n", "C12722\t104\t+\tTACGT\t0.500\t2.00\t1\t2\t1\t1\t0.095\t0.905\r\n", "C12722\t134\t+\tTGCGG\t0.500\t2.00\t1\t2\t2\t2\t0.095\t0.905\r\n", "C12768\t103\t+\tTTCGT\t0.167\t6.00\t1\t6\t6\t6\t0.030\t0.564\r\n", "C12768\t119\t+\tTTCGT\t0.250\t4.00\t1\t4\t4\t4\t0.046\t0.699\r\n", "C12768\t145\t+\tTTCGT\t0.000\t3.00\t0\t3\t3\t3\t0.000\t0.562\r\n", "C12768\t161\t+\tTTCGT\t0.000\t1.00\t0\t1\t1\t1\t0.000\t0.793\r\n", "C12778\t114\t+\tAGCGG\t0.000\t1.00\t0\t1\t1\t1\t0.000\t0.793\r\n", "C12782\t75\t+\tCGCGT\t0.000\t1.00\t0\t1\t0\t0\t0.000\t0.793\r\n" ] } ], "prompt_number": 33 }, { "cell_type": "code", "collapsed": false, "input": [ "cd " ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ "/Volumes/web/cnidarian/BiGo_larvae_merge/CgM3_[0316_1207]\n" ] } ], "prompt_number": 5 }, { "cell_type": "code", "collapsed": false, "input": [ "!grep \"[A-Z][A-Z]CG[A-Z]\" mk_methratio_out_CG.txt \n" ], "language": "python", "metadata": {}, "outputs": [], "prompt_number": 6 }, { "cell_type": "code", "collapsed": false, "input": [ "!awk '$8 >= 5' mk_methratio_out_CG5x.txt" ], "language": "python", "metadata": {}, "outputs": [], "prompt_number": 7 }, { "cell_type": "code", "collapsed": false, "input": [ "cd /Volumes/web/cnidarian/BiGo_larvae_merge/CgT1D3_[0316_1306]/\n" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ "/Volumes/web/cnidarian/BiGo_larvae_merge/CgT1D3_[0316_1306]\n" ] } ], "prompt_number": 8 }, { "cell_type": "code", "collapsed": false, "input": [ "!grep \"[A-Z][A-Z]CG[A-Z]\" mk_methratio_out_CG.txt \n" ], "language": "python", "metadata": {}, "outputs": [], "prompt_number": 9 }, { "cell_type": "code", "collapsed": false, "input": [ "!awk '$8 >= 5' mk_methratio_out_CG5x.txt" ], "language": "python", "metadata": {}, "outputs": [], "prompt_number": 10 }, { "cell_type": "code", "collapsed": false, "input": [ "cd /Volumes/web/cnidarian/BiGo_larvae_merge/CgT1D5_[0316_1346]/\n" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ "/Volumes/web/cnidarian/BiGo_larvae_merge/CgT1D5_[0316_1346]\n" ] } ], "prompt_number": 11 }, { "cell_type": "code", "collapsed": false, "input": [ "!grep \"[A-Z][A-Z]CG[A-Z]\" mk_methratio_out_CG.txt \n" ], "language": "python", "metadata": {}, "outputs": [], "prompt_number": 12 }, { "cell_type": "code", "collapsed": false, "input": [ "!awk '$8 >= 5' mk_methratio_out_CG5x.txt" ], "language": "python", "metadata": {}, "outputs": [], "prompt_number": 13 }, { "cell_type": "code", "collapsed": false, "input": [ "cd /Volumes/web/cnidarian/BiGo_larvae_merge/CgT3D3_[0316_1436]/\n" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ "/Volumes/web/cnidarian/BiGo_larvae_merge/CgT3D3_[0316_1436]\n" ] } ], "prompt_number": 14 }, { "cell_type": "code", "collapsed": false, "input": [ "!grep \"[A-Z][A-Z]CG[A-Z]\" mk_methratio_out_CG.txt \n" ], "language": "python", "metadata": {}, "outputs": [], "prompt_number": 15 }, { "cell_type": "code", "collapsed": false, "input": [ "!awk '$8 >= 5' mk_methratio_out_CG5x.txt" ], "language": "python", "metadata": {}, "outputs": [], "prompt_number": 16 }, { "cell_type": "code", "collapsed": false, "input": [ "cd /Volumes/web/cnidarian/BiGo_larvae_merge/CgT3D5_[0316_1532]/\n" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ "/Volumes/web/cnidarian/BiGo_larvae_merge/CgT3D5_[0316_1532]\n" ] } ], "prompt_number": 17 }, { "cell_type": "code", "collapsed": false, "input": [ "!grep \"[A-Z][A-Z]CG[A-Z]\" mk_methratio_out_CG.txt \n" ], "language": "python", "metadata": {}, "outputs": [], "prompt_number": 18 }, { "cell_type": "code", "collapsed": false, "input": [ "!awk '$8 >= 5' mk_methratio_out_CG5x.txt" ], "language": "python", "metadata": {}, "outputs": [], "prompt_number": 19 }, { "cell_type": "code", "collapsed": false, "input": [ "!head mk_methratio_out_CG5x.txt" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ "C12722\t104\t+\tTACGT\t1.000\t1.00\t1\t1\t1\t1\t0.207\t1.000\r\n", "C12722\t134\t+\tTGCGG\t1.000\t1.00\t1\t1\t1\t1\t0.207\t1.000\r\n", "C12768\t103\t+\tTTCGT\t1.000\t1.00\t1\t1\t1\t1\t0.207\t1.000\r\n", "C12768\t119\t+\tTTCGT\t1.000\t1.00\t1\t1\t1\t1\t0.207\t1.000\r\n", "C12778\t34\t+\tCTCGC\t0.000\t1.00\t0\t1\t1\t1\t0.000\t0.793\r\n", "C12778\t52\t+\tTTCGA\t0.000\t2.00\t0\t2\t2\t2\t0.000\t0.658\r\n", "C12778\t114\t+\tAGCGG\t0.000\t1.00\t0\t1\t1\t1\t0.000\t0.793\r\n", "C12780\t100\t+\tGACGT\t0.000\t1.00\t0\t1\t1\t1\t0.000\t0.793\r\n", "C12780\t144\t+\tATCGA\t0.000\t2.00\t0\t2\t2\t2\t0.000\t0.658\r\n", "C12788\t86\t+\tCTCGA\t0.000\t1.00\t0\t1\t1\t1\t0.000\t0.793\r\n" ] } ], "prompt_number": 20 }, { "cell_type": "heading", "level": 2, "metadata": {}, "source": [ "methylkit it" ] }, { "cell_type": "code", "collapsed": false, "input": [ "/Volumes/web/cnidarian/BiGo_larvae_merge/CgM1_[0316_0954]/\n", "/Volumes/web/cnidarian/BiGo_larvae_merge/CgM3_[0316_1207]/\n", "/Volumes/web/cnidarian/BiGo_larvae_merge/CgT1D3_[0316_1306]/\n", "/Volumes/web/cnidarian/BiGo_larvae_merge/CgT1D5_[0316_1346]/\n", "/Volumes/web/cnidarian/BiGo_larvae_merge/CgT3D3_[0316_1436]/\n", "/Volumes/web/cnidarian/BiGo_larvae_merge/CgT3D5_[0316_1532]/\n" ], "language": "python", "metadata": {}, "outputs": [] }, { "cell_type": "code", "collapsed": false, "input": [ "cd /Volumes/web/cnidarian/BiGo_larvae_merge/CgM1_[0316_0954]/\n" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ "/Volumes/web/cnidarian/BiGo_larvae_merge/CgM1_[0316_0954]\n" ] } ], "prompt_number": 21 }, { "cell_type": "code", "collapsed": false, "input": [ "!/Volumes/web/Mollusk/bs_larvae_exp/methratio.awk.sh \\\n", "mk_methratio_out_CG5x.txt > mk_CgM1.txt" ], "language": "python", "metadata": {}, "outputs": [], "prompt_number": 22 }, { "cell_type": "code", "collapsed": false, "input": [ "pwd" ], "language": "python", "metadata": {}, "outputs": [ { "metadata": {}, "output_type": "pyout", "prompt_number": 25, "text": [ "u'/Volumes/web/cnidarian/BiGo_larvae_merge/CgM1_[0316_0954]'" ] } ], "prompt_number": 25 }, { "cell_type": "code", "collapsed": false, "input": [ "!head mk_methratio_out_CG5x.txt" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ "C12706\t69\t+\tTCCGC\t0.000\t1.00\t0\t1\t1\t1\t0.000\t0.793\r\n", "C12706\t71\t+\tCGCGT\t0.000\t1.00\t0\t1\t1\t1\t0.000\t0.793\r\n", "C12722\t104\t+\tTACGT\t0.500\t2.00\t1\t2\t1\t1\t0.095\t0.905\r\n", "C12722\t134\t+\tTGCGG\t0.500\t2.00\t1\t2\t2\t2\t0.095\t0.905\r\n", "C12768\t103\t+\tTTCGT\t0.167\t6.00\t1\t6\t6\t6\t0.030\t0.564\r\n", "C12768\t119\t+\tTTCGT\t0.250\t4.00\t1\t4\t4\t4\t0.046\t0.699\r\n", "C12768\t145\t+\tTTCGT\t0.000\t3.00\t0\t3\t3\t3\t0.000\t0.562\r\n", "C12768\t161\t+\tTTCGT\t0.000\t1.00\t0\t1\t1\t1\t0.000\t0.793\r\n", "C12778\t114\t+\tAGCGG\t0.000\t1.00\t0\t1\t1\t1\t0.000\t0.793\r\n", "C12782\t75\t+\tCGCGT\t0.000\t1.00\t0\t1\t0\t0\t0.000\t0.793\r\n" ] } ], "prompt_number": 24 }, { "cell_type": "code", "collapsed": false, "input": [], "language": "python", "metadata": {}, "outputs": [] } ], "metadata": {} } ] }