This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Searching For A Mouse Gtf That Includes Cds, Tss, And Promoters.

I am looking for a mouse gtf to run with cufflinks that includes data on genes, isoforms, promoters, cds, and tss. So far, I have only been able to locate a gtf with data on genes, isoforms, and cds.

Thanks.

rna-seq gtf cuffdiff cufflinks
• 3,799 views • link
updated by Istvan Albert Istvan Albert • written by Eric • Eric

where did you look so far? I just checked out Ensembl Mouse, and indeed couldn't work out how to get regulatory features into gtf - you might have some luck mailing the Ensembl helpdesk to see if this is possible? In my experience they reply quickly and very usefully.

• 0 views • link
written by aidan-budd aidan-budd

1 answer

GTF is a gene transfer format and as such it is supposed to be limited to describing genes. You may be able to coerce other features to look like genes but I think there is a chance that this would invalidate the results of some of the tools and techniques that you want to employ later. Those too may have been built to expect input from genes.

• 122 views • link
written by Istvan Albert Istvan Albert

Log in to answer this question.

More posts like this