Question

Searching For A Mouse Gtf That Includes Cds, Tss, And Promoters.

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11.9 years ago

Eric ▴ 90

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 • 3.2k views

ADD COMMENT • link updated 11.9 years ago by Istvan Albert 102k • written 11.9 years ago by Eric ▴ 90

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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.

ADD REPLY • link 11.9 years ago by aidan-budd 1.9k

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cross-posted: http://stackoverflow.com/questions/14747059

ADD REPLY • link 11.9 years ago by Pierre Lindenbaum 164k

score 1 · Answer 1 · 2013-02-07

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.