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Gaius-Augustus / BRAKER

BRAKER is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET/EP/ETP and AUGUSTUS in novel eukaryotic genomes
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--softmasking_off #762

Closed TCHeaven closed 7 months ago

TCHeaven commented 7 months ago

I'm a little confused by the --softmasking_off flag, does braker perform masking itself by default? or is this flag to do with the reading of a masked file?

I have softmasked my genome already, before providing it to braker, should I use this flag? Will it make no difference?

KatharinaHoff commented 7 months ago

Do not use the option, input the softmasked genome.

It would make a difference, but probably make predictions worse.