sraFastqExtractor

Overview

Extract FASTQ files from prefetched SRA data using fasterq-dump. Supports both public and controlled-access (dbGaP) data.

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Usage

sraFastqExtractor.sh

sbatch --job-name=[jobName] ~/atelier/bin/sraFastqExtractor.sh -l [accessionList] [options]

Options

Option	Description
-l [accessionList]	Text file containing SRA accession IDs (one ID per line). Assumes accessions are in subdirectories with prefetched .sra files
-b [baseDir]	ase directory containing accession subdirectories (default: current directory)
-n [ngcFile]	Path to .ngc file for dbGaP controlled-access data
-d	Dry run
-v	Verbose output with debug logging
-h	Display help message

Examples

Basic extraction from public data

sbatch --job-name=fastq-extract ~/atelier/bin/sraFastqExtractor.sh \
    -l accessions.txt

Extract controlled-access data

sbatch --job-name=fastq-dbgap ~/atelier/bin/sraFastqExtractor.sh \
    -l accessions.txt \
    -n ~/prj_1234.ngc

Dry run preview

sbatch --job-name=fastq-preview ~/atelier/bin/sraFastqExtractor.sh \
    -l accessions.txt \
    -d

Verbose/debug mode

sbatch --job-name=fastq-verbose ~/atelier/bin/sraFastqExtractor.sh \
    -l accessions.txt \
    -v

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