[maker-devel] Filtering gene models based on eAED scores

[Carson Holt]

The eAED score also take protein reading frame into account and it can infers support for exons when both introns are validated (i.e. can be lower than AED in some cases). For your case where eAED is 1 but AED less than 1 means that you evidence support is from an overlapping protein, but it is never in the same reading frame as the gene model. So the positive evidence support may be suspect, or it may be real and the model is poor because of the assembly, gaps, etc. To use eAED instead in the quality_filter.pl script, you would have to to manually edit the script and replace ‘_AED' with ‘_eAED’. Using eAED instead will greatly drop sensitivity on lower quality assemblies (places where the predictors make the best model they can and not the correct model because the assembly won’t allow for the correct model but there is evidence that there is a gene locus). So make sure to always view suspect regions in browser first.

—Carson



> On Jun 9, 2018, at 2:06 PM, Federico López <flopezo84 at gmail.com> wrote:
> 
> Hello,
> 
> I'm using MAKER's "quality_filter.pl <http://quality_filter.pl/>" with the default option (AED<1). However, I have noticed cases in which models have low AED scores and high eAED scores (1.00), so presumably the good AED scores are the result of spurious evidence alignments. Is there a way to filter models based on eAED scores too?
> 
> Thank you.
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