Penn SCAP-T Pipeline: Documentation
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Module: RUM
This module will run the RUM aligner. The RUM alignment program must be installed separately (see Requires below).
Usage:
ngs.sh rum [-i inputDir] -p numProc -s species [-se] sampleID
Input:
sampleID/INPUTDIR/unaligned_1.fq
sampleID/INPUTDIR/unaligned_2.fq (paired-end reads)
Output:
sampleID/rum/sampleID.rum.sorted.bam (all aligned reads)
sampleID/rum/sampleID.rum.unique.bam (uniquely aligned reads)
Requires:
RUM ( http://cbil.upenn.edu/RUM )
samtools ( http://samtools.sourceforge.net/ )
Options:
-i inputDir - location of source files (default: trim).
-p numProc - number of cpu to use.
-s species - species from repository: /lab/repo/resources/rum2.
-se - single-end reads (default: paired-end)
Runs RUM using the trimmed files from sampleID/trim. Output is stored in sampleID/rum directory. No non-default options are specified for RUM.