Question

Is it possible to bulk download files from GEO repository?

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6 months ago

WUSCHEL ▴ 810

I am interested in accessing raw RNASeq data files from published manuscripts that are host in Gene Expression Omnibus. Is it possible to download them in bulk rather one by one?

Also is it possible to upload data to Galaxy directly from GEO?

Thank you for considering my request.

RNA-seq Galaxy Tanscriptomics • 551 views

ADD COMMENT • link updated 6 months ago by noodle ▴ 590 • written 6 months ago by WUSCHEL ▴ 810

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Galaxy specific requests are best posted on their help forum: https://help.galaxyproject.org/

ADD REPLY • link 6 months ago by GenoMax 147k

score 1 · Answer 1 · 2024-04-29

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6 months ago

atharvakarkare14 ▴ 40

Try using this library GEOparse

ADD COMMENT • link 6 months ago by atharvakarkare14 ▴ 40

score 1 · Answer 2 · 2024-04-29

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6 months ago

noodle ▴ 590

Also try the NCBI AWS bucket transfer tool. It's extremely convenient, however it's not instantaneous and you need to have a (paid) AWS account.

ADD COMMENT • link 6 months ago by noodle ▴ 590