[maker-devel] why no prediction

[陈文博]

Thank you for the help

I double checked the  "EST alignment", and sorry that the darkest pink is
the assembled transcript using Trinity, not EST. The splice sits is GT/AG.
The cufflinks and Trinity result suggest that this region could transcript.
There is a intact ORF in the prediction given by Ausgustus. Maybe this
region should be a real gene, however it was not predicted by Maker.

Thanks,
Wenbo



2015-05-12 20:31 GMT-04:00 Mark Yandell <myandell at genetics.utah.edu>:

> and finally check the splice sites for the EST splice are they valid
> GT/AG  or AT/AC?
>
>
> On May 12, 2015, at 4:18 PM, Carson Holt <carsonhh at gmail.com> wrote:
>
> > Also protein evidence will only be considered as support if it is in the
> same reading frame as the ab initio prediction. Complete mismatch of
> reading frames usually suggests a repeat like region.
> >
> > —Carson
> >
> >
> >> On May 12, 2015, at 4:16 PM, Carson Holt <carsonhh at gmail.com> wrote:
> >>
> >> The structure of the evidence appears to suggest a spurious prediction
> randomly overlapped by a spurious EST alignment. You would need at least
> protein evidence overlap to make it believable.  There is heavy discordance
> among the gene predictors. Also the fact that the gene would be 90% plus
> UTR if the EST does in fact represent true expression is a big factor.
> More likely it’s a pseudogene or semi repetitive region. Not making this a
> gene was the right call.
> >>
> >> —Carson
> >>
> >>
> >>
> >>> On May 12, 2015, at 3:56 PM, 陈文博 <chenwenbo1020 at gmail.com> wrote:
> >>>
> >>> Hi guys,
> >>>
> >>> I come with a wired case that one region in genome has evidence, but
> no gene prediction generated. Here are the detail.
> >>>
> >>>
> >>> <image.png>
> >>> color means:
> >>> pink: Augustus
> >>> light green: SNAP
> >>> dark pink: pred_gff
> >>> light yellow: cufflinks
> >>> darkest pink: EST alignment
> >>> dark yellow: protein alignment
> >>>
> >>> In the region marked by red frame, there are predictions from Augustus
> and pred_gff, also evidences from cufflinks, why there is no gene model
> generated? I could find the gene model in the
> "XXXX.all.maker.non_overlapping_ab_initio.transcripts.fasta" file. It is
> wired because it did have evidence supported.
> >>>
> >>> Could anyone know the reason?
> >>>
> >>> Thanks very much!
> >>>
> >>> Best,
> >>> Wenbo
> >>> _______________________________________________
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> >>> maker-devel at box290.bluehost.com
> >>>
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
> >>
> >
> >
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>
>
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