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

[Surya Saha]

Hi Carson,

We have been using AED as a primary metric for evaluating predictions in
our group but it sounds like we should be using both eAED and AED. Is there
a detailed explanation of how exactly eAED and AED are computed besides
Table 2 in the Cantarel 2008 paper? Thanks

-Surya

On Wed, Jun 13, 2018 at 2:03 PM Carson Holt <carsonhh at gmail.com> wrote:

> 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" 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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-- 

Surya Saha
Sol Genomics Network
Boyce Thompson Institute, Ithaca, NY, USA
https://citrusgreening.org/ <http://www.linkedin.com/in/suryasaha>
http://www.linkedin.com/in/suryasaha
https://twitter.com/SahaSurya
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