NAME
make_bed.py - find methylation in nanopore reads
DESCRIPTION
/usr/lib/python3/dist-packages/joblib/_multiprocessing_helpers.py:53: UserWarning: [Errno 13] Permission denied. joblib will operate in serial mode
- warnings.warn('%s.
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joblib will operate in serial mode' % (e,))
usage: make_bed.py [-h] [-d MIN_READ_DEPTH] [-t MOD_THRESHOLD] -f MCALLER_FILE
-
[-p POSITIONS] [--control] [--gff] [--ref REF] [--plot] [--plotsummary] [--plotdir PLOTDIR] [--vo] [-v]
Produce bed file of methylated positions based on mCaller output
optional arguments:
- -h, --help
-
show this help message and exit
- -d MIN_READ_DEPTH, --min_read_depth MIN_READ_DEPTH
-
minimum coverage of position to determine methylation (default = 15)
- -t MOD_THRESHOLD, --mod_threshold MOD_THRESHOLD
-
minimum fraction of observations with probability of methylation >=50% at a position to include in report (default = 0.5)
- -f MCALLER_FILE, --mCaller_file MCALLER_FILE
-
the output file from mCaller to summarize
- -p POSITIONS, --positions POSITIONS
-
~bed file of positions for which to calculate % of methylated reads (chromosome,start,end,strand); ignores other thresholds
- --control
-
take unmethylated positions as a control for motif detection
- --gff
-
output PacBio-style gff instead of bed ("identificationQv" score will be average probability of methylation)
- --ref REF
-
use reference fasta to output longer contexts surrounding a base, from -20 to +20
- --plot
-
plot currents deviations at the positions included (not recommended for many positions)
- --plotsummary
-
plot currents deviations summarized across the positions included
- --plotdir PLOTDIR
-
output directory for plots, default=mCaller_position_plots
- --vo
-
verbose output including probabilities for each position
- -v, --version
-
print version