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Old 05-30-2013, 01:11 AM   #1
Susanna5
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Location: Netherlands

Join Date: Apr 2013
Posts: 5
Default Downloading multiple SRA runs

Hello, I'm having some difficulties downloading multiple runs from an experiment in SRA. I don't want *all* the runs, or all the data from the experiment. I just want a selection I can give myself. I've googled about, and tried the idea of saving the selected runs to a cvs file by file>summary. and then running this command:
sed 1d sra_result.csv | cut -f14 | wget -i-

after observing the error of no URL, I checked the csv file summary, thinking I got the wrong column. Opening the csv file showed the runs, and the 14th entry was indeed the URL, but the entire file was not separating properly. I then added the separator to the beginning of the file:
sep=","
That still didn't work. It seems a novice problem, has anyone had it and/or know how to solve it?

I know of aspera, but that also seemed to be single files from the download guide example:
anonftp@ftp-trace.ncbi.nlm.nih.gov:2...96072.lite.sra

(I do have aspera installed) What I've tried is downloading a directory, so something like:
anonftp@ftp-trace.ncbi.nlm.nih.gov:22/sra/sra-instant/reads/ByRun/litesra/SRR/SRR096
and also (maybe silly but getting desperate) tried this
anonftp@ftp-trace.ncbi.nlm.nih.gov:22/sra/sra-instant/reads/ByRun/litesra/SRR/SRR096/SRR096072-SRR096075
trying to use their download example for my own purposes..
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Old 05-30-2013, 03:34 AM   #2
GenoMax
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Location: East Coast USA

Join Date: Feb 2008
Posts: 7,030
Default

Try this:

Code:
wget -r -nd -nH ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads//ByRun/litesra/SRR/SRR096
This will get all accessions # in the SRR096 directory.
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Old 05-30-2013, 07:01 AM   #3
muthu545
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Location: san antonio

Join Date: Jul 2011
Posts: 32
Default

Hi,

The Code suggested by GenoMax is very useful. I'm just providing a modification of the code:

Store the SRR096001-SRR096999 #s that would want to download in a file:
for example:
cat > SRR_2_download
SRR096023
SRR096072
SRR096074

for i in $(cat SRR_2_download);do wget -r -nd -nH ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByRun/litesra/SRR/SRR096/$i/*; done

This will download the specific SRA files that are listed in the file SRR_2_download

Thanks
--
Muthu
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