Penn SCAP-T Pipeline: Documentation
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Module: BARCODE
Runs kmerFind.py to select reads with a specific barcode sequence, optionally trimming with -c.
Usage: ngs.sh barcode [-i inputDir] [-t numProc] [-p] [-c contaminantsFile] [-m minLen] [-q phredThreshold] [-rN] [-rAT numBases] [-se] sampleID Input: /lab/repo/resources/trim/contaminants.fa (file containing contaminants) sampleID/inputDir/unaligned_1.fq sampleID/inputDir/unaligned_2.fq (paired-end reads) Output: sampleID/trim/unaligned_1.fq sampleID/trim/unaligned_2.fq (paired-end reads) sampleID/trim/sampleID.trim.stats.txt sampleID/trim/contaminants.fa (contaminants file) Requires: trimReads.py ( https://github.com/safisher/ngs ) Options: -i inputDir - location of source files (default: init). -t numProc - maximum number of cpu to use. -c - Cut reads at the barcode point. Read 1 will be cut from the barcode to the 3' end, read 2 will be cut from the barcode to the 5' end. -m - Mask the barcode portion of reads. Sequences on both sides of the barcode will remain unchanged. -l length - length of reads -pre prefix - sequence to be inserted before barcode sequence (default: none) -suf suffix - sequence to be inserted after barcode sequence (default: none) -m [AND|OR] - if a both a prefix and a suffix is given, whether to look for reads with [prefix][barcode][suffix] (AND), or reads with either [prefix][barcode] or [barcode][suffix] (OR). -se - single-end reads (default: paired-end)
Selected/trimmed data is placed in 'sampleID/barcode.trim'.