[maker-devel] augustus underpredicting

[Carson Holt]

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 <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

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