Question: How to download SRA fastq filese
0
gravatar for 110300553
23 months ago by
1103005530
1103005530 wrote:

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?

command line sra • 1.1k views
ADD COMMENTlink modified 23 months ago by Pierre Lindenbaum120k • written 23 months ago by 1103005530
2
gravatar for Pierre Lindenbaum
23 months ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum120k wrote:

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
ADD COMMENTlink written 23 months ago by Pierre Lindenbaum120k

Thank you so much!

ADD REPLYlink written 23 months ago by 1103005530

Can you explain this ? -O -

ADD REPLYlink written 23 months ago by Vijay Lakhujani4.1k

save to standard output

ADD REPLYlink written 23 months ago by Pierre Lindenbaum120k
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