How to download all the possible RNA-seq data sets from public data bases?
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7.8 years ago
Naim.Mahi ▴ 40

Dear all,

I want to write a function in R that will download all possible RNA-Seq data sets and sample annotations from public data bases such as GEO. Is there any package that will do it? I know SRAdb or GEOquery but I need to provide SRR or GSM number. I would really appreciate any help regarding this issue. TIA.

RNA-Seq R GEO next-gen sequencing • 1.6k views
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7.8 years ago
Ar ★ 1.1k

Use SRA Run Selector. This will provide you the SRA run table. And, then for download use sra-dump and then write a small script & automate the process. Good luck!

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