Question: Extract GEO for certain experiment type
0
gravatar for mariafirulevabio
11 days ago by
mariafirulevabio30 wrote:

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.

ADD COMMENTlink modified 11 days ago • written 11 days ago by mariafirulevabio30
1
gravatar for genomax
11 days ago by
genomax70k
United States
genomax70k wrote:

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.
ADD COMMENTlink modified 11 days ago • written 11 days ago by genomax70k

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?

ADD REPLYlink modified 10 days ago • written 10 days ago by mariafirulevabio30
1

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

ADD REPLYlink written 10 days ago by genomax70k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 2068 users visited in the last hour