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How can I programmatically download the GEO DataSets of a given accession?

I would like to download all the .sra files associated with this experiment (GSE55335). I can do it manually via the website but would like to be able to download them from a script or a terminal. I've downloaded and tried both the sra-toolkit and Entrez direct, but I've not managed to use either successfully for this task. Thank you.

sra entrez damid-seq geo
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updated by Ram Ram • written by James Ashmore James Ashmore

Have you tried GEOquery from the Bioconductor?

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updated by Ram Ram • written by PoGibas PoGibas

2 answers

Have a look at How to download raw sequence data from GEO/SRA

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written by Ying W Ying W

The SRAdb Bioconductor package is useful for this type of thing.

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written by Sean Davis Sean Davis

You can do it with R bioconductor. just google it you will see package to load and example on how you can get it done. i will also recommend you download R in a nutshell there is exact example there.

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written by tg • tg

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