[maker-devel] Curious pattern in AED distributions

[Mark Yandell]

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:
[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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