Question: Searching For A Mouse Gtf That Includes Cds, Tss, And Promoters.
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gravatar for Eric
2.6 years ago by
Eric80
Eric80 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.

gtf cufflinks cuffdiff rna-seq • 728 views
ADD COMMENTlink modified 2.6 years ago by Istvan Albert ♦♦ 56k • written 2.6 years ago by Eric80

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 2.6 years ago by aidan-budd1.8k

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

ADD REPLYlink written 2.6 years ago by Pierre Lindenbaum74k
1
gravatar for Istvan Albert
2.6 years ago by
Istvan Albert ♦♦ 56k
University Park, USA
Istvan Albert ♦♦ 56k 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 2.6 years ago • written 2.6 years ago by Istvan Albert ♦♦ 56k
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