Category
Generic
Usage
maskOutFa in.fa maskFile out.fa.masked
Manual
This tool is part of UCSC Genome Browser's utilities.
where in.fa and out.fa.masked can be the same file, and
maskFile can end in .out (for RepeatMasker) or .bed.
MaskFile parameter can also be the word 'hard' in which case
lower case letters are converted to N's.
options:
-soft - puts masked parts in lower case other in upper.
-softAdd - lower cases masked bits, leaves others unchanged
-clip - clip out of bounds mask records rather than dying.
-maskFormat=fmt - "out" or "bed" for when input does not have required extension.
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