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Old 06-21-2019, 10:04 AM   #2
Richard Finney
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Location: bethesda

Join Date: Feb 2009
Posts: 700
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Here's an easy way to do it, though not quite a one liner ...

1) go to the "run selector" for your project of interest:

https://www.ncbi.nlm.nih.gov/Traces/...re&query_key=2


2) Download "runinfo table" (to a file called SraRunTable.txt )

3) create url based on SRR id . example: wget ftp://ftp-trace.ncbi.nih.gov/sra/sra.../SRR001115.sra , use these URLS to wget in a script , like this ...

cat SraRunTable.txt | cut -f10 | awk '{print "wget ftp://ftp-trace.ncbi.nih.gov/sra/sra-instant/reads/ByRun/sra/SRR/"substr($1,1,6)"/"$1"/"$1".sra"}' | bash


Note that "cut -f10' is the field with the SRR ids.

Last edited by Richard Finney; 06-21-2019 at 10:14 AM.
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