[maker-devel] Pre-masked Genome for MAKER annotation

[Maggie Sudo]

Dear Sir /Madam,

I am using MAKER to annotate my genome. I have created a custom repeat
library for my genome and am wondering what is the appropriate
method/strategy to include it in my MAKER annotation.

 I was following the strategy described by Daren in the MAKER google
group.  (https://groups.google.com/u/1/g/maker-devel/c/patU-l_TQUM?pli=1).
So it seems the ideal strategy (if RepeatMasking is performed outside of
MAKER) would be to remove the simple/low complexity repeats in the
RepeatMasker GFF file and feed MAKER with the complex repeats only, then
have MAKER to run RepeatMasking to remake the simple repeats.

For some reason, I couldn't get MAKER to run RepeatMasker; as a result, I
couldn't remake the simple repeats using MAKER. The way I get around this
is by feeding MAKER the soft-masked genome (using -xsmall) that I got from
my RepeatMasker run, and the RepeatMasker GFF3 that contains* only complex
repeats*.

Does this make sense or do I need to include the simple repeats annotation
in the RepeatMasker GFF3 as well (which would result in the simple repeats
being hard masked because anything that comes from GFF3 will be hard
masked)?

I hope to hear from you soon. I would really appreciate your input in this.

Sincerely,
Maggie.
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