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

# compare\_genomes(1)

find methylation in nanopore reads

## NAME

compare\_genomes.py - find methylation in nanopore reads

## DESCRIPTION

usage: compare\_genomes.py \[-h\] **--bed1** BED1 **--bed2** BED2 \[-g GENOME\_ALIGNMENT\]

-

  \[-v\]

Compare methylation between two genomes by probabilities of methylation for aligned positions

### optional arguments:

- **-h**, **--help**

  show this help message and exit

- **--bed1** BED1

  bed file 1 with verbose output from make\_bed.py

- **--bed2** BED2

  bed file 2 with verbose output from make\_bed.py

- **-g** GENOME\_ALIGNMENT, **--genome\_alignment** GENOME\_ALIGNMENT

  an xmfa file from mauve (if absent, alignments assumed to be to the same reference genome)

- **-v**, **--version**

  print version