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