Downloading raw fastq data from NCBI SRA

• Go to PRJNA (for example: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA656645)
• Click  "299" under Number of links for row SRA Experiments

• Click "RunInfo" under, file and "Create File"

• We need SRR numbers, something like this:

• Assuming the above SRR accessions are in a file (SRR.list), we can run the following command:

time for d in $(cat SRR.list); do time prefetch -v $d; done &

• Now, we convert the sra file to fastq:

time for d in $(ls */*.sra);do fastq-dump --outdir fastq --split-files $d; done