[maker-devel] Question about pre-masked genome.

[Marc Tollis]

Hello,
I have a genome that has been well-annotated for species-specific repeats
(using RepeatModeler, trf, and RepeatMasker), and was wondering if I could
simply use the soft-masked assembly for maker annotation, in order to skip
the sometimes cumbersome repeatmasking step. Is this generally looked upon
as doable, or should I just stick with using the unmasked assembly and the
repeatmasking as bundled with my maker installation?

P.S. - as a spoiler, I already tried this (for snap training), but could
not confirm that the masked assembly (i.e., lowercase letters) was
maintained in the scaffolds as viewed in the maker output directory.
Thanks,
Marc
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