How to download SRA fastq filese

Question

[110300553]

I've generated a csv file with the run info for a bioproject SRA using the command:

wget 'http://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?save=efetch&rettype=runinfo&db=sra&term=PRJNA223640' -O - | tee SraRunInfo.csv Which I found in this answer C: download all samples from a study in BioProject

but could anyone help me with how I can use this csv file to download the files?

Answer 1

[Pierre Lindenbaum]

use NCBI fastq-dump

wget -O -  "http://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?save=efetch&rettype=runinfo&db=sra&term=PRJNA223640" | cut -d ',' -f 1 | grep -v '^$' |while read A; do  fastq-dump $A ; done

[110300553]

Thank you so much!

[lakhujanivijay]

Can you explain this ? -O -

[Pierre Lindenbaum]

save to standard output