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

[Jia-Xing Yue]

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> 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> 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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> > maker-devel at box290.bluehost.com
> > http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>
>


-- 
Jia-Xing Yue

Population Genomics and Complex Traits Group
Tour Pasteur 8eme etage
Faculté de Médecine
Institute for Research on Cancer and Aging, Nice (IRCAN)
CNRS UMR 7284 - INSERM U 1081 - Université Côte d’Azur (UCA)
28 Avenue de Valombrose
<https://maps.google.com/?q=28+Avenue+de+Valombrose&entry=gmail&source=g>
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France

Twitter: @iAmphioxus <https://twitter.com/iAmphioxus>
Personal website: http://www.iamphioxus.org/
Lab website: https://litilab.wordpress.com/
Yeast Population Reference Panel:
https://yjx1217.github.io/Yeast_PacBio_2016/welcome/
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