Download fastq data from NCBI SRA

Step 0

hpcf_interactive -q standard -R "rusage[mem=4000]"

Step 1. Put SRA accession IDs in a file, one per line.

nano sra_data.list

Copy and paste your SRA IDs.

SRR7633094
SRR7633093
SRR7633095
SRR7633096
SRR036758
SRR036759
SRR036760
SRR3721861
SRR3721862
SRR3721854
SRR3721853
SRR5367842

Control + o save.

Control + x exit.

Step 2

module load sra_toolkit/2.8.1.3

dos2unix sra_data.list

for i in `cat sra_data.list`; do echo $i; prefetch -v $i; fastq-dump --outdir . --split-files ~/ncbi/public/sra/$i.sra;done

The output fastq files will be, for example, SRR5367842.fastq. Please remember to rename it using the metainfo.

Note

“The problem with SRA is that a fair number of uploaded datasets are simply crap, i.e., people uploaded poorly formatted or incorrect data. For all ERR* datasets, do not use SRA. Download the original fastq files from ENA. If those have different numbers of reads then that’s what was uploaded.””

code @ github.