wig2bed.py - convert densities to intervals¶
Purpose¶
define intervals based on densities within a bigwig file.
The script currently implements the following methods (--method
):
- threshold
output windows that contain values above a certain threshold.
- std-above-mean
output windows that are a certain number of standard deviations above the mean.
- multiple-of-mean
output windows that are a certain times above the mean.
Usage¶
Bigwig files need to be supplied by the –bigwig-file options.
For example:
python wig2bed.py --threshold=10 --method=threshold --genome-file=mm10 --bigwig-file=in.bw > out.bed
Command line options¶
usage: wig2bed [-h] [-m {threshold,stddev-above-mean,multiple-of-mean}]
[-g GENOME_FILE] [-t THRESHOLD] [-i bigwig]
[--timeit TIMEIT_FILE] [--timeit-name TIMEIT_NAME]
[--timeit-header] [--random-seed RANDOM_SEED] [-v LOGLEVEL]
[--log-config-filename LOG_CONFIG_FILENAME]
[--tracing {function}] [-? ?] [-I STDIN] [-L STDLOG]
[-E STDERR] [-S STDOUT]
wig2bed: error: argument -?: expected one argument