---
name: "make_bed"
section: "1"
platform: "linux"
package: "mcaller"
version: "1.0.3+git20210624.b415090-3"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/make_bed"
---

# make\_bed(1)

find methylation in nanopore reads

## 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