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

[Daniel Ence]

Hi Marc, Several groups have been doing what you described with fungal genomes for a while and it seems to be working for them.  With the softmasked genome, maker will still allow EST alignments to extend into the masked regions; if it were a hard masked genome, this wouldn’t be possible.

Let us know how it works out though!

Thanks,
Daniel


On Mar 13, 2015, at 3:48 PM, Marc Tollis <mtollis at asu.edu<mailto:mtollis at asu.edu>> wrote:

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

--
Marc Tollis, Ph.D.
Post-Doctoral Research Associate
Arizona State University
LSE 313
(480) 965-7456
marc.tollis at asu.edu<mailto:marc.tollis at asu.edu>

website: https://sites.google.com/site/tollisresearch/
blog: anolistollis.wordpress.com<http://anolistollis.wordpress.com/>
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