Penn SCAP-T Pipeline: Documentation
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Module: BOWTIE
Align reads using Bowtie.
Usage:
ngs.sh bowtie [-i inputDir] [-v mismatches] [-m maxMulti] [-minins minInsertSize] [-maxins maxInsertSize] -p numProc -s species [-se] sampleID
Input:
sampleID/inputDir/unaligned_1.fq
sampleID/inputDir/unaligned_2.fq (paired-end reads)
Output:
sampleID/bowtie/sampleID.sorted.bam
sampleID/bowtie/sampleID.suppressed.sorted.bam
sampleID/bowtie/sampleID.stats.txt
Requires:
bowtie ( http://bowtie-bio.sourceforge.net/index.shtml )
samtools ( http://samtools.sourceforge.net/ )
Options:
-i inputDir - directory with unaligned reads (default: trim)
-v mismatches - maximum mismatches allowed per read length (default: 3)
-m maxMulti - suppress all alignments if > m alignments (default: 1)
-minins minInsertSize - minimum insert size for PE alignment (default: 250bp)
-maxins maxInsertSize - maximum insert size for PE alignment (default: 450bp)
-p numProc - number of cpu to use
-s species - species from repository: /lab/repo/resources/bowtie
-se - single-end reads (default: paired-end)
Run bowtie on the unaligned reads (ie sampleID/inputDir). The arguments used assume Bowtie version 1. Output is placed in the directory sampleID/bowtie. Multimapping reads that exceed the maxMulti count are output to the sampleID.suppressed.sorted.bam file (ie the Bowtie -max flag is used to direct the reads to this file). For paired-end samples, after the paired mapping is complete then all unmapped reads are aligned as if they were single-end with the alignments stored in the sampleID/bowtie/SE_mapping directory. The alignment stats for the single-end and paired-end mappings are reported in the stats file.