Entering edit mode
17 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
I don't think you can use EntrezDirect to download sequence data or are you referring to something else?
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.
Neither
esearch
orefetch
(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?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.