Penn SCAP-T Pipeline: Documentation
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Module: FASTQC
This module will run FastQC on the specified fastq files.
Usage:
ngs.sh fastqc [-i inputDir] [-o outputDir] [-se] sampleID
Input:
sampleID/inputDir/unaligned_1.fq
sampleID/inputDir/unaligned_2.fq (paired-end reads)
Output:
sampleID/outputDir/SAMPLEID.read_1.outputDir.html
sampleID/outputDir/SAMPLEID.read_2.outputDir.html (paired-end reads)
Requires:
FastQC ( http://www.bioinformatics.babraham.ac.uk/projects/fastqc/ )
Options:
-i inputDir - location of source file (default: init).
-i outputDir - location of output files (default: fastqc). If this is changed from the default, then it will not be accessible by the STATS module.
-se - single-end reads (default: paired-end)
Run FastQC on sampleID/inputDir/unaligned_1.fq and if PE also on sampleID/inputDir/unaligned_2.fq. FastQC only uses one input file so it is run twice in the case of pair-end reads.