.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.16.
.TH COMPARE_GENOMES.PY "1" "June 2021" "compare_genomes.py 1.0.3+git20210331.f7a616a" "User Commands"
.SH NAME
compare_genomes.py \- find methylation in nanopore reads
.SH DESCRIPTION
usage: compare_genomes.py [\-h] \fB\-\-bed1\fR BED1 \fB\-\-bed2\fR BED2 [\-g GENOME_ALIGNMENT]
.IP
[\-v]
.PP
Compare methylation between two genomes by probabilities of methylation for
aligned positions
.SS "optional arguments:"
.TP
\fB\-h\fR, \fB\-\-help\fR
show this help message and exit
.TP
\fB\-\-bed1\fR BED1
bed file 1 with verbose output from make_bed.py
.TP
\fB\-\-bed2\fR BED2
bed file 2 with verbose output from make_bed.py
.TP
\fB\-g\fR GENOME_ALIGNMENT, \fB\-\-genome_alignment\fR GENOME_ALIGNMENT
an xmfa file from mauve (if absent, alignments assumed
to be to the same reference genome)
.TP
\fB\-v\fR, \fB\-\-version\fR
print version