Entering edit mode
3.1 years ago
jobrien20
•
0
Hi, I'm trying to download multiple studies through esearch by providing a .txt file with the SRP names in, but for some reason the loop terminates after the first study. I was wondering if anyone knows how I can resolve this?
while read study
do
esearch -db sra -query ${study} | efetch --format runinfo | cut -d ',' -f 1 | grep SRR |
xargs fastq-dump --skip-technical \
--readids --read-filter pass --dumpbase \
--split-3 --outdir Output_folder/${study} --gzip
echo "${study} fastq files generated"
done < project_datas.txt
Did you verify that
esearch
is bringing back valid results for all queries? For many accessions you may want toprefetch
the data and then do dump.