[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,

Yes that's what I did actually. But it seems that I  only got much fewer
gene models for est2genome and protein2genome in this way than I  would
expect. I have turned on EVM for my maker run. Could this explain the low
numbers of est2genome and protein2genome models    that I got? Thx!

Best,
Jia-Xing

Sent from my Nokia Lumia 920
------------------------------
From: Carson Holt <carsonhh at gmail.com>
Sent: ‎30/‎01/‎2018 18:06
To: Jia-Xing Yue <yuejiaxing at gmail.com>
Cc: maker-devel at yandell-lab.org List <maker-devel at yandell-lab.org>
Subject: Re: [maker-devel] Is it possible to extract the GFF3 file for the
raw gene models predicted by est2genome and protein2genome?

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> 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
> >
> >
> >
> > _______________________________________________
> > maker-devel mailing list
> > 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>
06107 NICE Cedex 2
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/
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://yandell-lab.org/pipermail/maker-devel_yandell-lab.org/attachments/20180130/4db8b79a/attachment-0002.html>