Download data from GEO/SRA using link
1
0
Entering edit mode
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

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

sra fastq geo • 2.4k views
ADD COMMENT
2
Entering edit mode
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.

ADD COMMENT
0
Entering edit mode

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

ADD REPLY

Login before adding your answer.

Traffic: 1569 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6