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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.
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<div class="">Let me know if that helps or if other issues arise. </div>
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<div class="">Thanks,</div>
<div class="">Daniel</div>
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<div class="">Daniel Ence<br class="">
Graduate Student<br class="">
Eccles Institute of Human Genetics<br class="">
University of Utah<br class="">
15 North 2030 East, Room 2100<br class="">
Salt Lake City, UT 84112-5330 </div>
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<div class="">On Jan 20, 2016, at 8:27 AM, Daren C. Card <<a href="mailto:daren.card@gmail.com" class="">daren.card@gmail.com</a>> wrote:</div>
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Hello all,
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<div class="">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.</div>
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<div class="">I see the thread at <a href="https://groups.google.com/forum/#!topic/maker-devel/7UbOIvwaaRM" class="">https://groups.google.com/forum/#!topic/maker-devel/7UbOIvwaaRM</a> 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.</div>
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<div class="">#1 is problematic due to the reasons above.</div>
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<div class="">#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.</div>
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<div class="">#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).</div>
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<div class="">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.</div>
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<div class="">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?</div>
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<div class="">Thanks in advance for any help.</div>
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<div class="">Daren</div>
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<div class="">Daren Card</div>
<div class="">Castoe Lab</div>
<div class="">University of Texas at Arlington</div>
<div class=""><a href="http://www.darencard.net/" class="">www.darencard.net</a></div>
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