[maker-devel] Curious pattern in AED distributions

[Lior Glick]

Dear Mark,
Thank you for the quick reply. I'm happy to see this ignites your interest
and am willing to endure your punishing questions (;
Before I answer them, I just want to make sure we're on the same page - as
far as I understand, lower AED scores indicate higher agreement with the
evidence, so the "good stuff" is actually left of the 0.5 surge. Am I
correct? Otherwise, this is a very poor annotation...
Now for the questions:
1) I did not make any filtrations so far, so single exon genes are included
as well. in fact, I'm exploring the results in order to develop some
criteria for filtering the genes. Would you suggest discarding single exon
genes?

2) My evidence consist of assembled transcripts, proteins and predicted
gene models (pred_gff).

3) As for repeats, I'm masking based on a repeats library obtained from a
previous publication, specific to my organism of interest.

Unfortunately, I didn't understand your final question. Could you please
explain what you mean by "final build"?

Hope these answers are helpful, and waiting to hear more thoughts.

Thanks again.


On Sun, Apr 7, 2019, 18:11 Mark Yandell <myandell at genetics.utah.edu> wrote:

> Hi Lior,
>
>
>
>
>
> Fun! The short answer is I don’t know. Obviously, the good stuff is on the
> right side of 0.5.
>
> That said, I can think of a couple of things to look into to explain the
> left side of the graph. Are you allowing single exon genes? Are you using
> RNA seq data, protein, or both? What about repeat masking? Are you doing
> it?  Do you have your own library?
>
>
>
> My first guess, would be low complexity/repeat sequences generating more
> or less random blastx hits across the genome…Carson, what do you think?
>
>
>
> And finally, what does the AED look like for the genes included in the
> final build?
>
>
>
>
>
> Sorry for all the questions, Lior. That’s your punishment for asking an
> interesting one. 😉
>
>
>
> --mark
>
>
>
>
>
> *From: *maker-devel <maker-devel-bounces at yandell-lab.org> on behalf of
> Lior Glick <liorglic at mail.tau.ac.il>
> *Date: *Sunday, April 7, 2019 at 7:26 AM
> *To: *"maker-devel at yandell-lab.org" <maker-devel at yandell-lab.org>
> *Subject: *[maker-devel] Curious pattern in AED distributions
>
>
>
> 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:
>
> [image: 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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