[maker-devel] augustus underpredicting

[Xabier Vázquez-Campos]

I did it that way and AUGUSTUS is predicting a more reasonable number of
genes, about 12500 in Maker, but about 19000 in the model assessment step.
In comparison, SNAP gives 16000 and GeneMark 19000.

I haven't found any reference about but, would it be a good idea to train
Augustus over the masked genome instead?
Thanks,



On 12 September 2017 at 02:50, Carson Holt <carsonhh at gmail.com> wrote:

> BUSCO may be generating too few models. BUSCO also identifies classes of
> conserved short genes that may not represent enough training diversity for
> your organism. Try running MAKER in protein2genome or est2genome mode, and
> then train with those results.
>
> —Carson
>
>
> On Sep 10, 2017, at 7:03 PM, Xabier Vázquez-Campos <xvazquezc at gmail.com>
> wrote:
>
> Hi,
> I have been annotating a fungal genome as usual, using Busco-trained
> Augustus (in addition to GeneMark and SNAP), but for some reason, Augustus
> is predicting a mere 207 genes compared to 15-20k from the other two.
> I've never had this problem. The genome has an unusual repeat content
> close to 50%, not sure if that might suppose a problem.
> Has anybody come up with any similar issue?
> I also asked to Busco developers if they have any idea
> https://gitlab.com/ezlab/busco/issues/49
> Cheers,
> Xabi
>
> --
> Xabier Vázquez-Campos, *PhD*
> *Research Associate*
> NSW Systems Biology Initiative
> School of Biotechnology and Biomolecular Sciences
> The University of New South Wales
> Sydney NSW 2052 AUSTRALIA
>
>
>


-- 
Xabier Vázquez-Campos, *PhD*
*Research Associate*
NSW Systems Biology Initiative
School of Biotechnology and Biomolecular Sciences
The University of New South Wales
Sydney NSW 2052 AUSTRALIA
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