Question: Download data from GEO/SRA using link
0
gravatar for rioualen
7 months ago by
rioualen390
France
rioualen390 wrote:

I can't seem to find an easy way to download raw data from GEO. Say I want these experiments:

https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE93506

There used to be links to download SRA files, but I can't find it anymore. The best i can do is to go to each and every sample page, get the SRX identifier, then look it up here : https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?exp=%09SRX2485100&cmd=search&m=downloads&s=seq

SRA

However even like this I can't find a link that I could use to download the data on some server using wget or such.

What's the way to do it now?

Thanks

fastq sra geo • 548 views
ADD COMMENTlink modified 7 months ago by genomax74k • written 7 months ago by rioualen390
2
gravatar for genomax
7 months ago by
genomax74k
United States
genomax74k wrote:

Use Phil Ewels SRA-explorer: https://ewels.github.io/sra-explorer/ (search with PRJNA360965[All Fields] ).

If you are sure the links to download SRA files are now missing then you can email NCBI help desk. NCBI site has become so sprawling that parts break during upgrades. They will fix them once pointed out though.

ADD COMMENTlink modified 7 months ago • written 7 months ago by genomax74k

I didn't know this tool, it does just the job! Thanks a lot.

ADD REPLYlink written 7 months ago by rioualen390
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