Maker genome softmask

Question

[sansan96]

Hi everyone,

I'm using MAKER for the first time to annotate a plant genome, however I have a couple of questions that I think are pretty simple. First, I made a pre-identified repeat elements with RepeatModeler and RepeatMasker through EarlGrey TE. The generated gff3 (plant_scaffolds.full_mask.complex.reformat.gff3 ) was put into "rm_gff" along with transcripts assembled with trinity and proteins, however, I'm confused on which genome I should add in each round of annotation. Should I use the softmask genome in each round of maker or the unmasked one (original)?

I would really appreciate your help.

[biofalconch]

Not very familiar with MAKER but it seems that it will consider those as hard masked, it seems to suggest that you should let MAKER handle it internally and provide a non-masked genome

Specifying the GFF3 annotation file for the annotated complex repeats (rm_gff) has the effect of hard masking these repeats so that they do not confound our ability to identify coding genes.