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Question: How To Download All Sra Samples At Once ?
13
6.9 years ago by
Spain

Dear Biostars,

As you may know SRA is a repository for all types of sequencing data. I often times have to do manual download by copying links of every SRA dataset by hand and use wget. I am wondering is there any simplest approach than manual copying of links ? Thanx in advance

For ex: How can I download all the data related to SRP026197 ? http://www.ncbi.nlm.nih.gov/sra?term=SRP026197

ADD COMMENT • link • modified 2.6 years ago by Federico Giorgi • 630 • written 6.9 years ago by biorepine • 1.5k

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1

Have you tried the SRAdb package from bioconductor? It's been a while, but I think it can be used to do that sort of thing.

ADD REPLY • link written 6.9 years ago by Devon Ryan ♦ 98k

Actually, SRA is the repository for sequence data, not GEO. There are links between the two databases, but your question is actually related to SRA.

ADD REPLY • link written 6.9 years ago by Sean Davis ♦ 26k

oh yeah you are right. I will edit my question. thanx

ADD REPLY • link written 6.9 years ago by biorepine • 1.5k

here is another solution A: How to download raw sequence data from GEO/SRA

ADD REPLY • link written 6.3 years ago by Istvan Albert ♦♦ 86k

when I run the code on my computer,I have a problem below,what is wrong?

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library(SRAdb)

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srafile=getSRAdbFile()

trying URL 'http://gbnci.abcc.ncifcrf.gov/backup/SRAmetadb.sqlite.gz'Content type 'application/x-gzip' length 1308358823 bytes (1247.7 Mb)opened URLdownloaded 1247.7 Mb

Unzipping...

Error in .local(drv, ...) : Could not connect to database:unable to open database file

ADD REPLY • link modified 4.8 years ago • written 4.8 years ago by Ada • 0

Perhaps you ran out of space in /tmp or the equivalent. Anyway, please post things like this as new questions.

ADD REPLY • link modified 4.8 years ago • written 4.8 years ago by Devon Ryan ♦ 98k