Question: Searching For A Mouse Gtf That Includes Cds, Tss, And Promoters.
0
gravatar for Eric
14 months ago by
Eric70
Eric70 wrote:

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.

ADD COMMENTlink modified 14 months ago by Istvan Albert ♦♦ 39k • written 14 months ago by Eric70

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 REPLYlink written 14 months ago by aidan-budd1.7k

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

ADD REPLYlink written 14 months ago by Pierre Lindenbaum58k
1
gravatar for Istvan Albert
14 months ago by
Istvan Albert ♦♦ 39k
University Park, USA
Istvan Albert ♦♦ 39k wrote:

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.

ADD COMMENTlink modified 14 months ago • written 14 months ago by Istvan Albert ♦♦ 39k
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