How to download SRA fastq filese
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4.3 years ago
110300553 • 0

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?

sra command line • 2.4k views
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4.3 years ago

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
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Thank you so much!

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Can you explain this ? -O -

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save to standard output

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