Category
Generic
Usage
findMotif [options] -motif=<acgt...> sequence
Manual
This tool is part of UCSC Genome Browser's utilities.
where:
sequence is a .fa , .nib or .2bit file or a file which is a list of sequence files.
options:
-motif=
- search for this specified motif (case ignored, [acgt] only)
-chr= - process only this one chrN from the sequence
-strand=<+|-> - limit to only one strand. Default is both.
-bedOutput - output bed format (this is the default)
-wigOutput - output wiggle data format instead of bed file
-verbose=N - set information level [1-4]
NOTE: motif must be longer than 4 characters, less than 17
-verbose=4 - will display gaps as bed file data lines to stderr
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