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Maker genome softmask

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.

maker genome softmask plant
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updated by biofalconch biofalconch • written by san96 • san96

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.

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written by biofalconch biofalconch

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