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Downloading Data

Getting raw Fastq from Public Repositories

This page covers how to download raw sequencing data from public repositories including the Sequence Read Archive (SRA).

SRA Toolkit

The SRA Toolkit is a collection of command-line tools for downloading and processing sequencing data from the NCBI Sequence Read Archive (SRA). It allows users to retrieve raw sequencing data in various formats, including FASTQ.

SRA accession numbers can be found from GEO repository pages, usually found at the bottom of the GEO page under SRA Run Selector.

The SRA toolkit can be loaded on the CCB with:

module load sratoolkit

Downloading FASTQ files from SRA

You can use the fastq-dump command to download FASTQ files from SRA using the SRA accession number. For example:

fastq-dump --split-files SRR1234567

# This will download the fastq that then have to be gzipped
for file in *.fastq ; do
    echo "G-zipping $file" ;
    gzip $file ;
done

You can also directly run Bowtie2 on SRA files without downloading them first using --sra-acc flag:

bowtie2 -x path_to_genome_index --sra-acc SRR1234567 -S SRR1234567.sam