Question: Need help in downloading CEL files for multiple datasets from GEO in one go
gravatar for sndbt123
3.2 years ago by
sndbt12310 wrote:

Hi, I have a list of GSE ids (say around 200) from GEO database, whose CEL files belonging to different GSE id, I need to download one after another. Can anyone share the script.

python rna-seq next-gen R geo • 1.2k views
ADD COMMENTlink modified 3.2 years ago • written 3.2 years ago by sndbt12310

See if this works. I will move it to an answer when you confirm.

Using NCBI eUtils (replace GSE number as needed, use another loop outside the one below for multiple searches):

for i in `esearch -db gds -query GSE92586 | efetch -format docsum | xtract -pattern DocumentSummary -element FTPLink`; do wget $i/suppl/*.gz ; done
ADD REPLYlink written 3.2 years ago by GenoMax96k
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