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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
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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.
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.
oh yeah you are right. I will edit my question. thanx
here is another solution A: How to download raw sequence data from GEO/SRA
when I run the code on my computer,I have a problem below,what is wrong?
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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
Error in .local(drv, ...) : Could not connect to database:unable to open database file
Perhaps you ran out of space in /tmp or the equivalent. Anyway, please post things like this as new questions.