Extract GEO for certain experiment type

Question

[mariafirulevabio]

Dear all,

Suppose I have a big list of GEO's corresponding certain experiment type (e.g., sc-RNA-seq).

How can I extract all GEO's for target experiment type (sc-RNA-seq, in this case) and, after comparison all available GEO with my list, extract direct links for files which are presented in selected GEO's.

I will be very grateful if you answer at least the first question.

Answer 1

[GenoMax]

Try this.

1. Visit this link at GEO.
2. Under Summary on the search page change to Summary text. Adjust number of results (~3256 at moment) and get results.
3. Grep Accession numbers.
4. Compare to your list using comm unix util.

[mariafirulevabio]

Hi genomax,

Thanks for your advice. I suppose I should not only 'scRNAseq' but other terms because after intersection my list (1315 elements) with the got list from I found only 4 common accession numbers.

Could you prompt me how I can get direct links to files that correspond to the accession numbers that are not in my original list?

[GenoMax]

Use sra-explorer application by Phil Ewel to get links for accession numbers you want to download. The process is described in this post: sra-explorer : find SRA and FastQ download URLs in a couple of clicks