apply previously run mask using .out file

[Blosberg]

From a previous execution of RepeatMasker, I have a file of the form [genome].repeatmasker.out

I still have the original fasta file [genome].fa, and I would like to apply the mask to it, resulting in something like [genome].hardmasked.fa where all the bases from [genome].fa in regions referred to by the .out file are converted to N. I cannot re-run Repeatmasker from scratch because I don't have access to some of the necessary database files. Is there any option to apply the .out file that I already have without re-running from scratch?

[jebrosen]

I think this answer can help: https://github.com/rmhubley/RepeatMasker/issues/82#issuecomment-706766289. Let us know if that route works for you!