From A Geo Gsm Id, How To Obtain The Corresponding Raw File(S) Hosted On Sra?

Question

[Nico]

We often refer to Sequencing libraries with the GSM number (from NCBI GEO). I'd love to find a way to obtain the corresponding information, on GEO (such as GSE number, or annotations / description / metadata) and on SRA (where the raw files are hosted (most of the time, that is...)). From SRA, I'd like all the numbers (SRR, SRP, SRR, SRX and whatnot), but most importantly an automated way of downloading the files, usually .fastq

I believe I can use the NCBI e-Utils (http://www.ncbi.nlm.nih.gov/geo/info/geo_paccess.html) for GEO, but I haven't find a way to link to SRA.

As I'd like to do it for >100 libraries, the most automated (or programmable), the better it is!

Any pointers?

Thanks,

Answer 1

[Sean Davis]

Check out these R packages:

• http://bioconductor.org/packages/release/bioc/html/SRAdb.html
• http://bioconductor.org/packages/release/bioc/html/GEOmetadb.html

They are pretty nice for doing this type of thing. SRAdb is probably where it sounds like you would want to start.

Sean

Fair advertising--I am one of the authors of the packages....