[maker-devel] choosing the right gene model

[Carson Holt]

Both transcript and protein evidence will go into the AED calculation for overlap support. So in both cases the chosen model had better overlap (protein evidence will not count toward the eAED overlap calculation if it is out of frame with the model it is supposed to be supporting). The larger merged model generates a clutering affect on it’s evidence, so it’s evidence set for AED calculation is slightly different than the SNAP and Augustus model would generate. In both cases, I think GeneMark is hurting more than it is helping. You may want to just drop it from the analysis (unless it’s a fungi, I often find GeneMark can have that affect).

—Carson


> On Oct 12, 2017, at 12:09 AM, Xabier Vázquez-Campos <xvazquezc at gmail.com> wrote:
> 
> Hi there,
> 
> I was visualising the annotations and I realised that in some cases, what it seems to be a gene is splitted according to one of the gene models, despite that the other 2, est2genome and prot2genome suggest that it isn't the case.
> 
> <split-gene.png>
> 
> Although the opposite also happens.
> 
> <merged-gene.png>
> ​
> For some reason, the "out of place" model is always (or almost) the one from Genemark.
> 
> How much weight does carry the RNAseq and protein data on this decision (if any)?
> How exactly is the final gene selected?
> 
> 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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