{ "cells": [ { "cell_type": "markdown", "metadata": {}, "source": [ "Updated file" ] }, { "cell_type": "code", "execution_count": 8, "metadata": { "collapsed": false }, "outputs": [], "source": [ "cp /Volumes/web-1/trilobite/Crassostrea_gigas_ensembl_tracks/Crassostrea_gigas.GCA_000297895.1.24.fa \\\n", "/Users/sr320/data-genomic/tentacle/" ] }, { "cell_type": "code", "execution_count": 10, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "\r\n", "BSMAP v2.74\r\n", "Usage:\tbsmap [options]\r\n", " -a query a file, FASTA/FASTQ/BAM format\r\n", " -d reference sequences file, FASTA format\r\n", " -o output alignment file, BSP/SAM/BAM format, if omitted, the output will be written to STDOUT in SAM format.\r\n", "\r\n", " Options for alignment:\r\n", " -s seed size, default=16(WGBS mode), 12(RRBS mode). min=8, max=16.\r\n", " -v if this value is between 0 and 1, it's interpreted as the mismatch rate w.r.t to the read length.\r\n", " otherwise it's interpreted as the maximum number of mismatches allowed on a read, <=15.\r\n", " example: -v 5 (max #mismatches = 5), -v 0.1 (max #mismatches = read_length * 10%)\r\n", " default=0.08.\r\n", " -g gap size, BSMAP only allow 1 continuous gap (insert or deletion) with up to 3 nucleotides\r\n", " default=0\r\n", " -w maximum number of equal best hits to count, <=1000\r\n", " -3 using 3-nucleotide mapping approach\r\n", " -B start from the Nth read or read pair, default: 1\r\n", " -E end at the Nth read or read pair, default: 4,294,967,295\r\n", " -I index interval, default=4\r\n", " -k set the cut-off ratio for over-represented kmers, default=5e-07\r\n", " example: -k 1e-6 means the top 0.0001% over-represented kmer will be skipped in alignment\r\n", " -p number of processors to use, default=8\r\n", " -D activating RRBS mapping mode and set restriction enzyme digestion sites. \r\n", " digestion position marked by '-', example: -D C-CGG for MspI digestion.\r\n", " default: none (whole genome shotgun bisulfite mapping mode)\r\n", " -S seed for random number generation used in selecting multiple hits\r\n", " other seed values generate pseudo random number based on read index number, to allow reproducible mapping results. \r\n", " default=0. (get seed from system clock, mapping results not resproducible.)\r\n", " -n [0,1] set mapping strand information. default: 0\r\n", " -n 0: only map to 2 forward strands, i.e. BSW(++) and BSC(-+), \r\n", " for PE sequencing, map read#1 to ++ and -+, read#2 to +- and --.\r\n", " -n 1: map SE or PE reads to all 4 strands, i.e. ++, +-, -+, -- \r\n", " -M set alignment information for the additional nucleotide transition. \r\n", " is in the form of two different nucleotides N1N2, \r\n", " indicating N1 in the reads could be mapped to N2 in the reference sequences.\r\n", " default: -M TC, corresponds to C=>U(T) transition in bisulfite conversion. \r\n", " example: -M GA could be used to detect A=>I(G) transition in RNA editing. \r\n", "\r\n", " Options for trimming:\r\n", " -q quality threshold in trimming, 0-40, default=0 (no trim)\r\n", " -z base quality, default=33 [Illumina is using 64, Sanger Institute is using 33]\r\n", " -f filter low-quality reads containing >n Ns, default=5\r\n", " -A 3-end adapter sequence, default: none (no trim)\r\n", " -L map the first N nucleotides of the read, default:144 (map the whole read).\r\n", "\r\n", " Options for reporting:\r\n", " -r [0,1] how to report repeat hits, 0=none(unique hit/pair only); 1=random one, default:1.\r\n", " -R print corresponding reference sequences in SAM output, default=off\r\n", " -u report unmapped reads, default=off\r\n", " -H do not print header information in SAM format output\r\n", "\r\n", " Options for pair-end alignment:\r\n", " -b query b file\r\n", " -m minimal insert size allowed, default=28\r\n", " -x maximal insert size allowed, default=500\r\n", "\r\n", " -h help\r\n", "\r\n" ] } ], "source": [ "!/Applications/bioinfo/BSMAP/bsmap-2.74/bsmap \\\n" ] }, { "cell_type": "code", "execution_count": 9, "metadata": { "collapsed": true }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "\n", "BSMAP v2.74\n", "Start at: Wed Apr 15 09:48:58 2015\n", "\n", "Input reference file: /Users/sr320/data-genomic/tentacle/Crassostrea_gigas.GCA_000297895.1.24.fa \t(format: FASTA)\n", "Load in 4424 db seqs, total size 4192198 bp. 0 secs passed\n", "total_kmers: 43046721\n", "Create seed table. 1 secs passed\n", "max number of mismatches: read_length * 8% \tmax gap size: 0\n", "kmer cut-off ratio: 5e-07\n", "max multi-hits: 100\tmax Ns: 5\tseed size: 16\tindex interval: 4\n", "quality cutoff: 0\tbase quality char: '!'\n", "min fragment size:28\tmax fragemt size:500\n", "start from read #1\tend at read #4294967295\n", "additional alignment: T in reads => C in reference\n", "mapping strand: ++,-+\n", "Single-end alignment(6 threads)\n", "Input read file: /Users/sr320/data-genomic/tentacle/20150414_trimmed_2212_lane2_1000ppm_CTTGTA.fastq.gz \t(format: gzipped FASTQ)\n", "Output file: /Users/sr320/data-genomic/tentacle/1000ppm_CTTGTA-en24-v01.sam\t (format: SAM)\n", "Thread #4: \t50000 reads finished. 3 secs passed\n", "Thread #0: \t100000 reads finished. 3 secs passed\n", 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reads finished. 460 secs passed\n", "Thread #4: \t53750000 reads finished. 460 secs passed\n", "Thread #0: \t53800000 reads finished. 461 secs passed\n", "Thread #3: \t53850000 reads finished. 461 secs passed\n", "Thread #5: \t53900000 reads finished. 462 secs passed\n", "Thread #1: \t53950000 reads finished. 462 secs passed\n", "Thread #2: \t54000000 reads finished. 462 secs passed\n", "Thread #4: \t54050000 reads finished. 463 secs passed\n", "Thread #0: \t54100000 reads finished. 463 secs passed\n", "Thread #3: \t54150000 reads finished. 464 secs passed\n", "Thread #5: \t54200000 reads finished. 464 secs passed\n", "Thread #1: \t54250000 reads finished. 464 secs passed\n", "Thread #2: \t54300000 reads finished. 465 secs passed\n", "Thread #4: \t54350000 reads finished. 465 secs passed\n", "Thread #0: \t54400000 reads finished. 466 secs passed\n", "Thread #3: \t54450000 reads finished. 466 secs passed\n", "Thread #5: \t54500000 reads finished. 467 secs passed\n", "Thread #1: 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#5: \t55400000 reads finished. 474 secs passed\n", "Thread #1: \t55450000 reads finished. 474 secs passed\n", "Thread #2: \t55500000 reads finished. 474 secs passed\n", "Thread #4: \t55550000 reads finished. 475 secs passed\n", "Thread #0: \t55600000 reads finished. 476 secs passed\n", "Thread #3: \t55650000 reads finished. 476 secs passed\n", "Thread #5: \t55700000 reads finished. 477 secs passed\n", "Thread #1: \t55750000 reads finished. 477 secs passed\n", "Thread #2: \t55800000 reads finished. 477 secs passed\n", "Thread #4: \t55850000 reads finished. 478 secs passed\n", "Thread #0: \t55900000 reads finished. 478 secs passed\n", "Thread #3: \t55950000 reads finished. 479 secs passed\n", "Thread #5: \t56000000 reads finished. 479 secs passed\n", "Thread #1: \t56050000 reads finished. 479 secs passed\n", "Thread #2: \t56100000 reads finished. 480 secs passed\n", "Thread #4: \t56150000 reads finished. 480 secs passed\n", "Thread #0: \t56200000 reads finished. 481 secs passed\n", "Thread #3: \t56250000 reads finished. 481 secs passed\n", "Thread #5: \t56300000 reads finished. 482 secs passed\n", "Thread #1: \t56350000 reads finished. 482 secs passed\n", "Thread #2: \t56400000 reads finished. 482 secs passed\n", "Thread #4: \t56450000 reads finished. 483 secs passed\n", "Thread #0: \t56500000 reads finished. 483 secs passed\n", "Thread #3: \t56550000 reads finished. 484 secs passed\n", "Thread #5: \t56600000 reads finished. 484 secs passed\n", "Thread #1: \t56650000 reads finished. 484 secs passed\n", "Thread #2: \t56700000 reads finished. 484 secs passed\n", "Thread #4: \t56750000 reads finished. 485 secs passed\n", "Thread #0: \t56800000 reads finished. 486 secs passed\n", "Thread #3: \t56850000 reads finished. 486 secs passed\n", "Thread #5: \t56900000 reads finished. 486 secs passed\n", "Thread #1: \t56950000 reads finished. 487 secs passed\n", "Thread #2: \t57000000 reads finished. 487 secs passed\n", "Thread #4: \t57050000 reads finished. 487 secs passed\n", "Thread #0: \t57100000 reads finished. 488 secs passed\n", "Thread #3: \t57150000 reads finished. 489 secs passed\n", "Thread #5: \t57200000 reads finished. 489 secs passed\n", "Thread #1: \t57250000 reads finished. 489 secs passed\n", "Thread #2: \t57300000 reads finished. 489 secs passed\n", "Thread #4: \t57350000 reads finished. 490 secs passed\n", "Thread #0: \t57400000 reads finished. 491 secs passed\n", "Thread #3: \t57450000 reads finished. 491 secs passed\n", "Thread #5: \t57500000 reads finished. 491 secs passed\n", "Thread #1: \t57550000 reads finished. 492 secs passed\n", "Thread #2: \t57600000 reads finished. 492 secs passed\n", "Thread #4: \t57650000 reads finished. 492 secs passed\n", "Thread #0: \t57700000 reads finished. 493 secs passed\n", "Thread #3: \t57750000 reads finished. 494 secs passed\n", "Thread #5: \t57800000 reads finished. 494 secs passed\n", "Thread #1: \t57850000 reads finished. 494 secs passed\n", "Thread #2: \t57900000 reads finished. 494 secs passed\n", "Thread #4: \t57950000 reads finished. 495 secs passed\n", "Thread #0: \t58000000 reads finished. 496 secs passed\n", "Thread #3: \t58050000 reads finished. 496 secs passed\n", "Thread #5: \t58100000 reads finished. 496 secs passed\n", "Thread #1: \t58150000 reads finished. 497 secs passed\n", "Thread #2: \t58200000 reads finished. 497 secs passed\n", "Thread #1: \t58413574 reads finished. 497 secs passed\n", "Thread #4: \t58250000 reads finished. 497 secs passed\n", "Thread #0: \t58300000 reads finished. 498 secs passed\n", "Thread #3: \t58350000 reads finished. 498 secs passed\n", "Thread #5: \t58400000 reads finished. 499 secs passed\n", "Total number of aligned reads: 43948 (0.075%)\n", "Done.\n", "Finished at Wed Apr 15 09:57:17 2015\n", "Total time consumed: 499 secs\n" ] } ], "source": [ "!/Applications/bioinfo/BSMAP/bsmap-2.74/bsmap \\\n", "-a /Users/sr320/data-genomic/tentacle/20150414_trimmed_2212_lane2_1000ppm_CTTGTA.fastq.gz \\\n", "-d /Users/sr320/data-genomic/tentacle/Crassostrea_gigas.GCA_000297895.1.24.fa \\\n", "-o /Users/sr320/data-genomic/tentacle/1000ppm_CTTGTA-en24-v01.sam \\\n", "-p 6 \n" ] }, { "cell_type": "code", "execution_count": 3, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "\n", "BSMAP v2.74\n", "Start at: Wed May 6 14:57:38 2015\n", "\n", "Input reference file: /Users/sr320/data-genomic/tentacle/Crassostrea_gigas.GCA_000297895.1.24.fa \t(format: FASTA)\n", "Load in 4424 db seqs, total size 4192198 bp. 0 secs passed\n", "total_kmers: 43046721\n", "Create seed table. 1 secs passed\n", "max number of mismatches: read_length * 8% \tmax gap size: 0\n", "kmer cut-off ratio: 5e-07\n", "max multi-hits: 100\tmax Ns: 5\tseed size: 16\tindex interval: 4\n", "quality cutoff: 0\tbase quality char: '!'\n", "min fragment size:28\tmax fragemt size:500\n", "start from read #1\tend at read #4294967295\n", "additional alignment: T in reads => C in reference\n", "mapping strand: ++,-+\n", "Single-end alignment(6 threads)\n", "Input read file: /Users/sr320/data-genomic/tentacle/20150414_trimmed_2212_lane2_1000ppm_CTTGTA.fastq \t(format: FASTQ)\n", "Output file: /Users/sr320/data-genomic/tentacle/1000ppm_CTTGTA-en24-v02.sam\t (format: SAM)\n", "Thread #0: \t50000 reads finished. 4 secs passed\n", "Thread #1: \t100000 reads finished. 4 secs passed\n", "Thread #3: \t150000 reads finished. 4 secs passed\n", "Thread #2: \t200000 reads finished. 4 secs passed\n", "Thread #5: \t250000 reads finished. 4 secs passed\n", "Thread #4: \t300000 reads finished. 4 secs passed\n", "Thread #0: \t350000 reads finished. 6 secs passed\n", "Thread #1: \t400000 reads finished. 6 secs passed\n", "Thread #3: \t450000 reads finished. 6 secs passed\n", "Thread #2: \t500000 reads finished. 6 secs passed\n", "Thread #5: \t550000 reads finished. 7 secs passed\n", "Thread #4: \t600000 reads finished. 7 secs passed\n", "Thread #0: \t650000 reads finished. 8 secs passed\n", "Thread #1: \t700000 reads finished. 9 secs passed\n", "Thread #3: \t750000 reads finished. 9 secs passed\n", "Thread #2: \t800000 reads finished. 9 secs passed\n", "Thread #5: \t850000 reads finished. 9 secs passed\n", "Thread #4: \t900000 reads finished. 9 secs passed\n", "Thread #0: \t950000 reads finished. 11 secs passed\n", "Thread #1: \t1000000 reads finished. 11 secs passed\n", "Thread #3: \t1050000 reads finished. 11 secs passed\n", "Thread #2: \t1100000 reads finished. 11 secs passed\n", "Thread #5: \t1150000 reads finished. 11 secs passed\n", "Thread #4: \t1200000 reads finished. 12 secs passed\n", "Thread #0: \t1250000 reads finished. 13 secs passed\n", "Thread #1: \t1300000 reads finished. 14 secs passed\n", "Thread #3: \t1350000 reads finished. 14 secs passed\n", "Thread #2: \t1400000 reads finished. 14 secs passed\n", "Thread #5: \t1450000 reads finished. 14 secs passed\n", "Thread #4: \t1500000 reads finished. 14 secs passed\n", "Thread #0: \t1550000 reads finished. 16 secs passed\n", "Thread #1: \t1600000 reads finished. 16 secs passed\n", "Thread #3: \t1650000 reads finished. 16 secs passed\n", "Thread #2: \t1700000 reads finished. 16 secs passed\n", "Thread #5: \t1750000 reads finished. 16 secs passed\n", "Thread #4: \t1800000 reads finished. 17 secs passed\n", "Thread #0: \t1850000 reads finished. 18 secs passed\n", "Thread #1: \t1900000 reads finished. 18 secs passed\n", "Thread #3: \t1950000 reads finished. 19 secs passed\n", "Thread #2: \t2000000 reads finished. 19 secs passed\n", "Thread #5: \t2050000 reads finished. 19 secs passed\n", "Thread #4: \t2100000 reads finished. 19 secs passed\n", "Thread #0: \t2150000 reads finished. 21 secs passed\n", "Thread #1: \t2200000 reads finished. 21 secs passed\n", "Thread #3: \t2250000 reads finished. 21 secs passed\n", "Thread #2: \t2300000 reads finished. 21 secs passed\n", "Thread #5: \t2350000 reads finished. 21 secs passed\n", "Thread #4: \t2400000 reads finished. 22 secs 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"Thread #1: \t55900000 reads finished. 466 secs passed\n", "Thread #3: \t55950000 reads finished. 466 secs passed\n", "Thread #2: \t56000000 reads finished. 467 secs passed\n", "Thread #5: \t56050000 reads finished. 467 secs passed\n", "Thread #4: \t56100000 reads finished. 467 secs passed\n", "Thread #0: \t56150000 reads finished. 468 secs passed\n", "Thread #1: \t56200000 reads finished. 468 secs passed\n", "Thread #3: \t56250000 reads finished. 469 secs passed\n", "Thread #2: \t56300000 reads finished. 469 secs passed\n", "Thread #5: \t56350000 reads finished. 470 secs passed\n", "Thread #4: \t56400000 reads finished. 470 secs passed\n", "Thread #0: \t56450000 reads finished. 470 secs passed\n", "Thread #1: \t56500000 reads finished. 471 secs passed\n", "Thread #3: \t56550000 reads finished. 471 secs passed\n", "Thread #2: \t56600000 reads finished. 471 secs passed\n", "Thread #5: \t56650000 reads finished. 472 secs passed\n", "Thread #4: \t56700000 reads finished. 472 secs passed\n", "Thread #0: \t56750000 reads finished. 473 secs passed\n", "Thread #1: \t56800000 reads finished. 473 secs passed\n", "Thread #3: \t56850000 reads finished. 474 secs passed\n", "Thread #2: \t56900000 reads finished. 474 secs passed\n", "Thread #5: \t56950000 reads finished. 475 secs passed\n", "Thread #4: \t57000000 reads finished. 475 secs passed\n", "Thread #0: \t57050000 reads finished. 475 secs passed\n", "Thread #1: \t57100000 reads finished. 476 secs passed\n", "Thread #3: \t57150000 reads finished. 476 secs passed\n", "Thread #2: \t57200000 reads finished. 476 secs passed\n", "Thread #5: \t57250000 reads finished. 477 secs passed\n", "Thread #4: \t57300000 reads finished. 477 secs passed\n", "Thread #0: \t57350000 reads finished. 478 secs passed\n", "Thread #1: \t57400000 reads finished. 478 secs passed\n", "Thread #3: \t57450000 reads finished. 479 secs passed\n", "Thread #2: \t57500000 reads finished. 479 secs passed\n", "Thread #5: \t57550000 reads finished. 479 secs passed\n", "Thread #4: \t57600000 reads finished. 480 secs passed\n", "Thread #0: \t57650000 reads finished. 480 secs passed\n", "Thread #1: \t57700000 reads finished. 480 secs passed\n", "Thread #3: \t57750000 reads finished. 481 secs passed\n", "Thread #2: \t57800000 reads finished. 481 secs passed\n", "Thread #5: \t57850000 reads finished. 482 secs passed\n", "Thread #4: \t57900000 reads finished. 482 secs passed\n", "Thread #0: \t57950000 reads finished. 483 secs passed\n", "Thread #1: \t58000000 reads finished. 483 secs passed\n", "Thread #3: \t58050000 reads finished. 483 secs passed\n", "Thread #2: \t58100000 reads finished. 484 secs passed\n", "Thread #5: \t58150000 reads finished. 484 secs passed\n", "Thread #4: \t58200000 reads finished. 485 secs passed\n", "Thread #5: \t58413574 reads finished. 485 secs passed\n", "Thread #0: \t58250000 reads finished. 485 secs passed\n", "Thread #1: \t58300000 reads finished. 485 secs passed\n", "Thread #3: \t58350000 reads finished. 486 secs passed\n", "Thread #2: \t58400000 reads finished. 486 secs passed\n", "Total number of aligned reads: 43903 (0.075%)\n", "Done.\n", "Finished at Wed May 6 15:05:44 2015\n", "Total time consumed: 486 secs\n" ] } ], "source": [ "!/Applications/bioinfo/BSMAP/bsmap-2.74/bsmap \\\n", "-a /Users/sr320/data-genomic/tentacle/20150414_trimmed_2212_lane2_1000ppm_CTTGTA.fastq \\\n", "-d /Users/sr320/data-genomic/tentacle/Crassostrea_gigas.GCA_000297895.1.24.fa \\\n", "-o /Users/sr320/data-genomic/tentacle/1000ppm_CTTGTA-en24-v02.sam \\\n", "-p 6 \n" ] }, { "cell_type": "code", "execution_count": 5, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "\n", "BSMAP v2.74\n", "Start at: Wed May 6 15:10:01 2015\n", "\n", "Input reference file: /Users/sr320/data-genomic/tentacle/Crassostrea_gigas.GCA_000297895.1.24.fa \t(format: FASTA)\n", "Load in 4424 db seqs, total size 4192198 bp. 0 secs passed\n", "total_kmers: 43046721\n", "Create seed table. 1 secs passed\n", "max number of mismatches: read_length * 8% \tmax gap size: 0\n", "kmer cut-off ratio: 5e-07\n", "max multi-hits: 100\tmax Ns: 5\tseed size: 16\tindex interval: 4\n", "quality cutoff: 0\tbase quality char: '!'\n", "min fragment size:28\tmax fragemt size:500\n", "start from read #1\tend at read #4294967295\n", "additional alignment: T in reads => C in reference\n", "mapping strand: ++,-+,+-,--\n", "Single-end alignment(8 threads)\n", "Input read file: /Users/sr320/data-genomic/tentacle/20150414_trimmed_2212_lane2_1000ppm_CTTGTA.fastq \t(format: FASTQ)\n", "Output file: /Users/sr320/data-genomic/tentacle/1000ppm_CTTGTA-en24-v03.sam\t (format: SAM)\n", "Thread #0: \t50000 reads finished. 4 secs passed\n", "Thread #3: \t100000 reads finished. 4 secs passed\n", "Thread #4: \t200000 reads finished. 4 secs passed\n", "Thread #1: \t150000 reads finished. 4 secs passed\n", "Thread #2: \t250000 reads finished. 5 secs passed\n", "Thread #7: \t300000 reads finished. 5 secs 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reads finished. 504 secs passed\n", "Thread #2: \t56450000 reads finished. 505 secs passed\n", "Thread #1: \t56500000 reads finished. 506 secs passed\n", "Thread #7: \t56550000 reads finished. 506 secs passed\n", "Thread #5: \t56600000 reads finished. 506 secs passed\n", "Thread #6: \t56650000 reads finished. 507 secs passed\n", "Thread #3: \t56700000 reads finished. 508 secs passed\n", "Thread #0: \t56750000 reads finished. 508 secs passed\n", "Thread #4: \t56800000 reads finished. 508 secs passed\n", "Thread #2: \t56850000 reads finished. 508 secs passed\n", "Thread #1: \t56900000 reads finished. 509 secs passed\n", "Thread #7: \t56950000 reads finished. 509 secs passed\n", "Thread #5: \t57000000 reads finished. 510 secs passed\n", "Thread #6: \t57050000 reads finished. 511 secs passed\n", "Thread #3: \t57100000 reads finished. 511 secs passed\n", "Thread #0: \t57150000 reads finished. 511 secs passed\n", "Thread #4: \t57200000 reads finished. 512 secs passed\n", "Thread #2: \t57250000 reads finished. 512 secs passed\n", "Thread #1: \t57300000 reads finished. 513 secs passed\n", "Thread #7: \t57350000 reads finished. 513 secs passed\n", "Thread #5: \t57400000 reads finished. 513 secs passed\n", "Thread #6: \t57450000 reads finished. 514 secs passed\n", "Thread #3: \t57500000 reads finished. 515 secs passed\n", "Thread #0: \t57550000 reads finished. 515 secs passed\n", "Thread #4: \t57600000 reads finished. 515 secs passed\n", "Thread #2: \t57650000 reads finished. 515 secs passed\n", "Thread #1: \t57700000 reads finished. 516 secs passed\n", "Thread #7: \t57750000 reads finished. 516 secs passed\n", "Thread #5: \t57800000 reads finished. 516 secs passed\n", "Thread #6: \t57850000 reads finished. 517 secs passed\n", "Thread #3: \t57900000 reads finished. 519 secs passed\n", "Thread #0: \t57950000 reads finished. 520 secs passed\n", "Thread #4: \t58000000 reads finished. 520 secs passed\n", "Thread #2: \t58050000 reads finished. 520 secs passed\n", "Thread #1: \t58100000 reads finished. 521 secs passed\n", "Thread #7: \t58150000 reads finished. 521 secs passed\n", "Thread #5: \t58200000 reads finished. 521 secs passed\n", "Thread #2: \t58413574 reads finished. 521 secs passed\n", "Thread #6: \t58250000 reads finished. 521 secs passed\n", "Thread #3: \t58300000 reads finished. 522 secs passed\n", "Thread #0: \t58350000 reads finished. 522 secs passed\n", "Thread #4: \t58400000 reads finished. 523 secs passed\n", "Total number of aligned reads: 268272 (0.46%)\n", "Done.\n", "Finished at Wed May 6 15:18:44 2015\n", "Total time consumed: 523 secs\n" ] } ], "source": [ "!/Applications/bioinfo/BSMAP/bsmap-2.74/bsmap \\\n", "-a /Users/sr320/data-genomic/tentacle/20150414_trimmed_2212_lane2_1000ppm_CTTGTA.fastq \\\n", "-d /Users/sr320/data-genomic/tentacle/Crassostrea_gigas.GCA_000297895.1.24.fa \\\n", "-o /Users/sr320/data-genomic/tentacle/1000ppm_CTTGTA-en24-v03.sam \\\n", "-n 1 \\\n", "-p 8 \n" ] }, { "cell_type": "code", "execution_count": 6, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "\r\n", "BSMAP v2.74\r\n", "Usage:\tbsmap [options]\r\n", " -a query a file, FASTA/FASTQ/BAM format\r\n", " -d reference sequences file, FASTA format\r\n", " -o output alignment file, BSP/SAM/BAM format, if omitted, the output will be written to STDOUT in SAM format.\r\n", "\r\n", " Options for alignment:\r\n", " -s seed size, default=16(WGBS mode), 12(RRBS mode). min=8, max=16.\r\n", " -v if this value is between 0 and 1, it's interpreted as the mismatch rate w.r.t to the read length.\r\n", " otherwise it's interpreted as the maximum number of mismatches allowed on a read, <=15.\r\n", " example: -v 5 (max #mismatches = 5), -v 0.1 (max #mismatches = read_length * 10%)\r\n", " default=0.08.\r\n", " -g gap size, BSMAP only allow 1 continuous gap (insert or deletion) with up to 3 nucleotides\r\n", " default=0\r\n", " -w maximum number of equal best hits to count, <=1000\r\n", " -3 using 3-nucleotide mapping approach\r\n", " -B start from the Nth read or read pair, default: 1\r\n", " -E end at the Nth read or read pair, default: 4,294,967,295\r\n", " -I index interval, default=4\r\n", " -k set the cut-off ratio for over-represented kmers, default=5e-07\r\n", " example: -k 1e-6 means the top 0.0001% over-represented kmer will be skipped in alignment\r\n", " -p number of processors to use, default=8\r\n", " -D activating RRBS mapping mode and set restriction enzyme digestion sites. \r\n", " digestion position marked by '-', example: -D C-CGG for MspI digestion.\r\n", " default: none (whole genome shotgun bisulfite mapping mode)\r\n", " -S seed for random number generation used in selecting multiple hits\r\n", " other seed values generate pseudo random number based on read index number, to allow reproducible mapping results. \r\n", " default=0. (get seed from system clock, mapping results not resproducible.)\r\n", " -n [0,1] set mapping strand information. default: 0\r\n", " -n 0: only map to 2 forward strands, i.e. BSW(++) and BSC(-+), \r\n", " for PE sequencing, map read#1 to ++ and -+, read#2 to +- and --.\r\n", " -n 1: map SE or PE reads to all 4 strands, i.e. ++, +-, -+, -- \r\n", " -M set alignment information for the additional nucleotide transition. \r\n", " is in the form of two different nucleotides N1N2, \r\n", " indicating N1 in the reads could be mapped to N2 in the reference sequences.\r\n", " default: -M TC, corresponds to C=>U(T) transition in bisulfite conversion. \r\n", " example: -M GA could be used to detect A=>I(G) transition in RNA editing. \r\n", "\r\n", " Options for trimming:\r\n", " -q quality threshold in trimming, 0-40, default=0 (no trim)\r\n", " -z base quality, default=33 [Illumina is using 64, Sanger Institute is using 33]\r\n", " -f filter low-quality reads containing >n Ns, default=5\r\n", " -A 3-end adapter sequence, default: none (no trim)\r\n", " -L map the first N nucleotides of the read, default:144 (map the whole read).\r\n", "\r\n", " Options for reporting:\r\n", " -r [0,1] how to report repeat hits, 0=none(unique hit/pair only); 1=random one, default:1.\r\n", " -R print corresponding reference sequences in SAM output, default=off\r\n", " -u report unmapped reads, default=off\r\n", " -H do not print header information in SAM format output\r\n", "\r\n", " Options for pair-end alignment:\r\n", " -b query b file\r\n", " -m minimal insert size allowed, default=28\r\n", " -x maximal insert size allowed, default=500\r\n", "\r\n", " -h help\r\n", "\r\n" ] } ], "source": [ "!/Applications/bioinfo/BSMAP/bsmap-2.74/bsmap \\\n" ] }, { "cell_type": "code", "execution_count": 8, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ ">1817 EMCGIT00000000820 C15560+ 110-182\r\n", "GATACATGTAGCTCAGTTGGTAGAGCACTTGACTAGAGATTCAGAGGGCCAGGTTCGAAT\r\n", "CCCACTTTGTTCC\r\n", ">11810 EMCGIT00000002018 C16282- 5-126\r\n", "TGTCAGAAGTGGGATTCGAACCCACGCCCACATTCGTGGACCAGAACACTCGCACTCTCG\r\n", "TGGTGAGAATGAAGAGTTATCGCTCTTGAGTCTGGCGCCTTAGACCGCTCGGCCATCCTG\r\n", "AC\r\n", ">22281 EKC17955 C16582- 35-385\r\n", "TCAGTTCGTTAGCGCAACCAATGCTTCCACAACGTCCCCATTGTGTTCTCGTAATGTCCG\r\n", "TTCAGCTATTTGTCTTGTTATTTCCATTTCCGCTACAATCAAATCAACATCTTCTTTGTT\r\n" ] } ], "source": [ "!head /Users/sr320/data-genomic/tentacle/Crassostrea_gigas.GCA_000297895.1.24.fa" ] }, { "cell_type": "code", "execution_count": 9, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "28631\r\n" ] } ], "source": [ "!fgrep -c \">\" /Users/sr320/data-genomic/tentacle/Crassostrea_gigas.GCA_000297895.1.24.fa" ] }, { "cell_type": "code", "execution_count": null, "metadata": { "collapsed": true }, "outputs": [], "source": [] } ], "metadata": { "kernelspec": { "display_name": "Python 2", "language": "python", "name": "python2" }, "language_info": { "codemirror_mode": { "name": "ipython", "version": 2 }, "file_extension": ".py", "mimetype": "text/x-python", "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython2", "version": "2.7.9" } }, "nbformat": 4, "nbformat_minor": 0 }