Sra-tools

From wiki
Revision as of 16:49, 23 March 2016 by Rf (talk | contribs)
Jump to: navigation, search

To load

module load sra-tools

the chief command for this toolbox is fastq-dump, which downloads the SRA you are looking for

Identifying the right SRA name is an issue, so it's good to be able to do a quick test to see if you have the name correct via

fastq-dump - X 5 -Z SRR390728

"-X 5" just downloads the first five reads, while "-Z" send them to STDOUT. If this doesn't return an error you can go ahead and download via

fastq-dump --split-files SRR390728