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3.2 years ago
rioualen ▴ 610

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

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

sra fastq geo • 2.4k views
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3.2 years ago
GenoMax 117k

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.

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