[maker-devel] augustus underpredicting

[Carson Holt]

Gene predictors tend to over predict, so I would not take the high numbers given by SNAP and GeneMark as true counts. You will probably end up with something like 7-10k in the final results. But now Augustus is giving a higher count, you should be good to start running MAKER.

—Carson




> On Sep 17, 2017, at 7:12 PM, Xabier Vázquez-Campos <xvazquezc at gmail.com> wrote:
> 
> 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 <mailto: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 <mailto: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
> 
> 
> 
> 
> -- 
> 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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