[maker-devel] Is it possible to extract the GFF3 file for the raw gene models predicted by est2genome and protein2genome?

[Carson Holt]

MAKER models will al have ‘maker’ in the source column. Everything else is a reference alignment (not a model). But you can grep on the gene name. If it is sourced from SNAP, it will have snap in the name, and the same is true for augustus, est2genome, protein2genome, etc.

—Carson


> On Jan 30, 2018, at 10:03 AM, Jia-Xing Yue <yuejiaxing at gmail.com> wrote:
> 
> Dear Carson,
> 
> Thanks for the quick response! Could you elaborate  a bit on on "grep on the name". Do you mean just grep all the lines in the gff_merge output with "est2genome" and "protein2genome" in column 3? In that case, what I got is the alignments rather than the gene model guessed by Maker based on the alignment, right? 
> 
> 
> Thanks!
> 
> Best,
> Jia-Xing
> 
> 
> 
> On Tue, Jan 30, 2018 at 5:57 PM, Carson Holt <carsonhh at gmail.com <mailto:carsonhh at gmail.com>> wrote:
> You can just grep on the name. Although est2genome and protein2genome should only be used for initial training, as they are almost always guaranteed to be partial and should be disabled once you have trained gene predictors that can build complete models.
> 
> —Carson
> 
> > On Jan 30, 2018, at 9:32 AM, Jia-Xing Yue <yuejiaxing at gmail.com <mailto:yuejiaxing at gmail.com>> wrote:
> >
> > Hello,
> >
> > I enabled the est2genome and protein2genome option for Maker-3.00.0-beta in my particular case. I was wondering if it is possible to extract the gene models predicted by snap, augustus, est2genome, and protein2genome respectively.
> >
> > By using the gff_merge command, I think I can extract some gene models for each cases but not all, especially for the est2genome and protein2genome set (e.g. those labeled with "maker-chr*-exonerate_est2genome-gene" and "maker-chr*-exonerate_protein2genome-gene").
> >
> > Thanks in advance!
> >
> > Best,
> > Jia-Xing
> >
> >
> >
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> 
> 
> 
> -- 
> Jia-Xing Yue 
> 
> Population Genomics and Complex Traits Group
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