Penn SCAP-T Pipeline: Documentation
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Module: INIT
This module will extract the raw reads file(s) from a repository and prepare them for processing.
Usage:
ngs.sh init [-i inputDir] [-se] sampleID
Input:
inputDir/sampleID/*_R1_*.gz
inputDir/sampleID/*_R2_*.gz (paired-end reads)
Output:
sampleID/init/unaligned_1.fq
sampleID/init/unaligned_2.fq (paired-end reads)
Options:
-i - parent directory containing subdirectory with compressed fastq files (default: ./raw). This is the parent directory of the sample-specific directory. The sampleID will be used to complete the directory path (ie inputDir/sampleID).
-se - single-end reads (default: paired-end)
By default this expects the directory './raw/sampleID' that contains the demultiplexed reads, for the sample called sampleID. The demultiplexed reads need to be gzipped. The files containing the first reads need to include '_R1_' in their filenames and the second read files need to contain '_R2_' in the filenames (note the placement of the underscores). If inputDir is used then the read files are expected to reside in 'inputDir/sampleID'.
This will uncompress the raw files and place them in the directory './sampleID/init. Output files are named 'unaligned_1.fq' (first reads) and 'unaligned_2.fq' (second reads). Only unaligned_1.fq will be generated in the case of single-end reads.