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.
              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