Question: How to download raw data in batch from NCBI based on Series Accession number or Platform ID
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gravatar for biolab
4 weeks ago by
biolab890
China
biolab890 wrote:

Dear all,

I have a list of NCBI GEO Series Accession numbers and Platform IDs, and want to download the raw data in batch. A previous post on Biostars presents a good example of batch download (How to download raw sequence data from GEO/SRA ), but that solution is based on project ID rather than GEO Series Accession number. Does anyone know how to work out this task? Thank you very much!

sra • 105 views
ADD COMMENTlink modified 4 weeks ago by genomax29k • written 4 weeks ago by biolab890

Can you post an example of the Accession number you are interested in? @Istvan's solution with eUtils should be able to accommodate your needs.

ADD REPLYlink written 4 weeks ago by genomax29k

Thank you for your comment, genomax! The GEO Series Accession Number is something like GSE65022, and the Platform ID is like GPL19657. I want to get the SRA number something like SRR4024915.

ADD REPLYlink modified 4 weeks ago • written 4 weeks ago by biolab890

This may be helpul batchentrez

ADD REPLYlink written 4 weeks ago by Buffo460

Hi, Buffo, thanks for your comment! However, after uploading a list of Platform ID (eg, GPL19657), I could not get the SAR run number, which is something like SRR4024915.

ADD REPLYlink written 4 weeks ago by biolab890
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