.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.16.
.TH MAKE_BED.PY "1" "June 2021" "make_bed.py 1.0.3+git20210331.f7a616a" "User Commands"
.SH NAME
make_bed.py \- find methylation in nanopore reads
.SH DESCRIPTION
\fI\,/usr/lib/python3/dist\-packages/joblib/_multiprocessing_helpers\/\fP.py:53: UserWarning: [Errno 13] Permission denied.  joblib will operate in serial mode
.TP
warnings.warn('%s.
joblib will operate in serial mode' % (e,))
.PP
usage: make_bed.py [\-h] [\-d MIN_READ_DEPTH] [\-t MOD_THRESHOLD] \fB\-f\fR MCALLER_FILE
.IP
[\-p POSITIONS] [\-\-control] [\-\-gff] [\-\-ref REF] [\-\-plot]
[\-\-plotsummary] [\-\-plotdir PLOTDIR] [\-\-vo] [\-v]
.PP
Produce bed file of methylated positions based on mCaller output
.SS "optional arguments:"
.TP
\fB\-h\fR, \fB\-\-help\fR
show this help message and exit
.TP
\fB\-d\fR MIN_READ_DEPTH, \fB\-\-min_read_depth\fR MIN_READ_DEPTH
minimum coverage of position to determine methylation
(default = 15)
.TP
\fB\-t\fR MOD_THRESHOLD, \fB\-\-mod_threshold\fR MOD_THRESHOLD
minimum fraction of observations with probability of
methylation >=50% at a position to include in report
(default = 0.5)
.TP
\fB\-f\fR MCALLER_FILE, \fB\-\-mCaller_file\fR MCALLER_FILE
the output file from mCaller to summarize
.TP
\fB\-p\fR POSITIONS, \fB\-\-positions\fR POSITIONS
~bed file of positions for which to calculate % of
methylated reads (chromosome,start,end,strand);
ignores other thresholds
.TP
\fB\-\-control\fR
take unmethylated positions as a control for motif
detection
.TP
\fB\-\-gff\fR
output PacBio\-style gff instead of bed
("identificationQv" score will be average probability
of methylation)
.TP
\fB\-\-ref\fR REF
use reference fasta to output longer contexts
surrounding a base, from \fB\-20\fR to +20
.TP
\fB\-\-plot\fR
plot currents deviations at the positions included
(not recommended for many positions)
.TP
\fB\-\-plotsummary\fR
plot currents deviations summarized across the
positions included
.TP
\fB\-\-plotdir\fR PLOTDIR
output directory for plots,
default=mCaller_position_plots
.TP
\fB\-\-vo\fR
verbose output including probabilities for each
position
.TP
\fB\-v\fR, \fB\-\-version\fR
print version