Category
Generic
Usage
trfBig inFile outFile
Manual
This tool is part of UCSC Genome Browser's utilities.
This will repeatedly run trf to mask tandem repeats in infile
and put masked results in outFile. inFile and outFile can be .fa
or .nib format. Outfile can be .bed as well. Sequence output is hard
masked, lowercase.
-bed creates a bed file in current dir
-bedAt=path.bed - create a bed file at explicit location
-tempDir=dir Where to put temp files.
-trf=trfExe explicitly specifies trf executable name
-maxPeriod=N Maximum period size of repeat (default 2000)
-keep don't delete tmp files
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