entrez direct private data access
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3 months ago
Synanth • 0

Hi, I'm trying to use the entrez cli utilities access and download run data from a pre-print. I have the GSE accession number and the access token-- but can't seem to find how to handle the query to be able to download the data in fastq. Any help would be greatly appreciated. Best, Synanth

geo entrez • 403 views
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I don't think you can use EntrezDirect to download sequence data or are you referring to something else?

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I should clarify: I want to use EntrezDirect to get and parse SRX numbers which I can then use with fastq-dump. I just don't know how to use the token in the parameters to gain access.

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Neither esearch or efetch (which is what you would typically use) seem to have command line options to include a token on the command line. Perhaps you need to set a system variable with the token like one does with NCBI_API_KEY?

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Thanks, I'll look into it more and just download the tar via the browser and use scp to transfer it to the workhorse for now.