[maker-devel] Passing pre-masked repeats into Maker

[Daniel Ence]

HI Daren, I think the solution you described sounds appropriate. If you’re concerned about how the simple repeats will be handled by maker in the gff, then you can just take those out. If they’re important for downstream analysis, you can add them back in then.

Let me know if that helps or if other issues arise.

Thanks,
Daniel

Daniel Ence
Graduate Student
Eccles Institute of Human Genetics
University of Utah
15 North 2030 East, Room 2100
Salt Lake City, UT 84112-5330

On Jan 20, 2016, at 8:27 AM, Daren C. Card <daren.card at gmail.com<mailto:daren.card at gmail.com>> wrote:

Hello all,

I’m about to use Maker to begin annotating a vertebrate genome. We use successive rounds of RepeatMasker to annotate repeats due to some library issues we’ve noticed with Repbase (at least in our critters) and to incorporate de novo repeats from RepeatModeler, a process I don’t think Maker could match. I’m wonder what the best way to pass these annotations into Maker would be.

I see the thread at https://groups.google.com/forum/#!topic/maker-devel/7UbOIvwaaRM nicely outlines what Maker does with repeats, and it looks like I have 3 options: (1) reannotate in Maker, (2) pass in a RepeatMasker GFF, or (3) pass in a masked genome.

#1 is problematic due to the reasons above.

#2 looks like it would hard mask the complex repeats like we want, but will also hard mask the simple repeats, which wouldn’t be ideal for evidence mapping from transcripts/proteins.

#3 is cautioned against in the link above, and without an accompanying GFF, I would imagine that Maker wouldn’t be able to release the masking to perform Exonerate polishing (Ns could be gaps or could be hard masking, it wouldn’t know).

The way I thought to get around these apparent issues (but let me know if my thinking is incorrect) is to separate simple and complex repeats from the final RepeatMasker GFF. Feed only the complex repeats into Maker as a GFF, so that they are hard masked and accounted for, and have Maker also run RepeatMasker, thus remaking the simple repeats (and maybe some other complex hits, primarily through RepeatRunner). Then Maker can presumedly release the masking as needed.

Would this type of workaround be a good idea or are there other options? Or am I just overthinking something that isn’t really a problem?

Thanks in advance for any help.

Daren

Daren Card
Castoe Lab
University of Texas at Arlington
www.darencard.net<http://www.darencard.net/>
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