[maker-devel] Question about adding UTR

[Brandi Cantarel]

Shane,
add_utr_gff, just adds lines in the gff file that say the boundaries for the "lower" and "upper" UTR.  Normally a program would use the difference between the exon boundaries and the CDS boundaries to determine the UTR, however some programs need this explicitly spelled out.

Brandi

On Feb 3, 2010, at 1:09 PM, Shane Brubaker wrote:

> Hi, I was wondering if someone could give me a little background on extending gene models to include more UTR.  I see a script called add_utr_gff.pl, but I'm not entirely clear on what this does.
> 
> Basically we have made gene models using MAKER and these were fed ESTs that come from NGS data, assembled using Velvet.  But we often see transcription that goes outside the boundaries of the gene.  When we do quantitative analysis of transcription using Cufflinks, we do not always get results as accurate as we would like, because part of the UTR is not in the gene model.
> 
> So I guess I'm wondering, does MAKER by default use the entire EST, and extend the gene model to include UTR?  If so then my main problem might be getting the ESTs themselves to be longer.
> 
> And what does add_utr_gff do, and do I need to use that?
> 
> What is the current status of plans for direct use of NGS data by Maker?
> 
> 
> Thanks so much for your help!
> 
> - Shane
> 
> 
> 
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