[maker-devel] Filtering of ab initio gene models

[Daniel Standage]

I do not provide Gap or Target attributes in the GFF3. Will this affect the
AED as well, or just the eAED?


--
Daniel S. Standage
Ph.D. Candidate
Computational Genome Science Laboratory
Indiana University


On Wed, Jun 4, 2014 at 3:09 PM, Carson Holt <carsonhh at gmail.com> wrote:

> Sure.  that would be helpful.  One question. Do you provide the Gap
> attribute in your precomputed alignments?  Having or not having that
> attribute affects the eAED score which takes reading frame into account,
> and may cause some things to be kept that normally would be dropped,
> because MAKER won't be able to take the points of mismatch of the alignment
> into account (it just assumes match everywhere).
>
> --Carson
>
>
> From: Daniel Standage <daniel.standage at gmail.com>
> Date: Wednesday, June 4, 2014 at 1:03 PM
> To: Maker Mailing List <maker-devel at yandell-lab.org>
> Subject: [maker-devel] Filtering of ab initio gene models
>
> Thanks everyone for your responses recently!
>
> The reason for my recent flurry of email activity is that I'm seeing some
> unexpected trends when running the new version of Maker with precomputed
> alignments. Compared with an annotation I did a while ago (Maker 2.10,
> Maker-computed alignments), this new annotation has a substantial number of
> new genes annotated. If I compare distributions of AED scores between the
> old and new annotation, it's clear that the new annotation has a lot more
> low-quality models. If I look at new gene models that do not overlap with
> any gene model from the old annotation, the likelihood that it's a
> low-quality model is much higher.
>
> I decided to run a little experiment. I annotated a scaffold first using
> Maker 2.10 and then using Maker 2.31.3. I both cases, I used the same
> pre-computed transcript and protein alignments and the same (latest)
> version of SNAP as the only *ab initio* predictor. Maker 2.10 predicted
> 44 genes while Maker 2.31.3 predicted 63. If we group gene models into loci
> by overlap, there are 33 loci with gene models from both 2.10 and 2.31.3, 1
> locus with only models from 2.10, and 28 loci with only models from 2.31.3.
>
> Before this experiment, I assumed the issue was related to providing
> pre-computed alignments in GFF3 format and perhaps violating some important
> assumption. However, this experiment makes me wonder whether there have
> been changes to how Maker filters *ab initio* gene models between version
> 2.10 and version 2.31.3? Do you have any ideas? If it would help, I could
> put together a small data set that reproduces the behavior I just described.
>
> Thanks!
>
> --
> Daniel S. Standage
> Ph.D. Candidate
> Computational Genome Science Laboratory
> Indiana University
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