[maker-devel] Curious pattern in AED distributions

[Carson Holt]

Yes. maker2zff tries to further select a subset of the best supported models by requiring multiple forms of evidence support.

—Carson


> On Apr 7, 2019, at 10:42 PM, Xabier Vázquez-Campos <xvazquezc at gmail.com> wrote:
> 
> 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 <mailto: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 <mailto: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!
> > _______________________________________________
> > maker-devel mailing list
> > maker-devel at box290.bluehost.com <mailto:maker-devel at box290.bluehost.com>
> > http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org <http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org>
> 
> 
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com <mailto:maker-devel at box290.bluehost.com>
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org <http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org>
> 
> 
> -- 
> 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

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://yandell-lab.org/pipermail/maker-devel_yandell-lab.org/attachments/20190407/7b400218/attachment-0003.html>