[maker-devel] Curious pattern in AED distributions

[Xabier Vázquez-Campos]

If you train SNAP, the maker2zff script has internal quality cutoffs based
on the existence of evidence. e.g. by default it will require having some
EST evidence

On Mon, 8 Apr 2019 at 11:32, Carson Holt <carsonhh at gmail.com> wrote:

> That’s interesting. It could be a handful of internal filters that help
> with spurious results.
>
> I use a 0.5 sensitivity/specificity to identify shared edges for a
> jaccardian split on overlapping evidence clusters for example. There are
> also a couple of places where if the only thing supporting a model is a
> single exon blastx hit (i.e. no exonerate, ab initio model, or est splice
> support, but just a chunk od single exon blastx) then maker will use a
> reading frame aware AED value of 0.5 as a filter (as in it checks if the
> reading frame matches and not just raw overlap). If that’s the case, the
> spike near 0.5 may indicate I needed to be a little strickter than my
> empirical cutoff estimate. Perhaps 0.4 or 0.45 would be the better cuttoff
> for these spurious blastx induced models.
>
> —Carson
>
>
> > On Apr 7, 2019, at 7:25 AM, Lior Glick <liorglic at mail.tau.ac.il> wrote:
> >
> > Hi MAKER users,
> > Lately I've been performing annotations for multiple genomes from the
> same species.
> > When plotting the histogram of AED scores over all genes, I repeatedly
> see a very specific pattern, that looks something like this:
> > <AED_hist.png>
> > This pattern is a bit surprising to me, in two aspects:
> > 1) Why is there a surge towards 0.5?
> > 2) Why is there a sudden drop right after that surge?
> >
> > Has anyone else seen this, or is this a specific outcome of my
> data/configuration?
> > Any ideas of what may cause such a distribution?
> >
> > While this is not necessarily an indication of a problem or bug, it does
> seem a bit odd, and  might imply some bias or artifact.
> > Would appreciate your comments.
> > Thank you!
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>
>
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-- 
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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