.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.4.
.TH MASON_METHYLATION "1" "June 2017" "mason_methylation 2.3.1+dfsg-4" "User Commands"
.SH NAME
mason_methylation \- Methylation Level Simulation
.PP
SYNOPSIS
.IP
mason_methylation [OPTIONS] \fB\-i\fR IN.fa \fB\-o\fR OUT.fa
.PP
DESCRIPTION
.IP
Simulate methylation levels for IN.fa and write them to OUT.fa.
.PP
OPTIONS
.HP
\fB\-h\fR, \fB\-\-help\fR
.IP
Display the help message.
.HP
\fB\-\-version\-check\fR BOOL
.IP
Turn this option off to disable version update notifications of the
application. One of 1, ON, TRUE, T, YES, 0, OFF, FALSE, F, and NO.
Default: 1.
.HP
\fB\-\-version\fR
.IP
Display version information.
.HP
\fB\-q\fR, \fB\-\-quiet\fR
.IP
Low verbosity.
.HP
\fB\-v\fR, \fB\-\-verbose\fR
.IP
Higher verbosity.
.HP
\fB\-vv\fR, \fB\-\-very\-verbose\fR
.IP
Highest verbosity.
.HP
\fB\-\-seed\fR INTEGER
.IP
Seed for RNG. Default: 0.
.HP
\fB\-i\fR, \fB\-\-in\fR INPUT_FILE
.IP
Input FASTA file with genome. Valid filetypes are: .fasta and .fa.
.HP
\fB\-o\fR, \fB\-\-out\fR INPUT_FILE
.IP
Input FASTA file with genome. Valid filetypes are: .fasta and .fa.
.IP
Methylation Level Simulation:
.HP
\fB\-\-methylation\-levels\fR
.IP
Enable methylation level simulation.
.HP
\fB\-\-meth\-cg\-mu\fR DOUBLE
.IP
Median of beta distribution for methylation level of CpG loci. In
range [0..1]. Default: 0.6.
.HP
\fB\-\-meth\-cg\-sigma\fR DOUBLE
.IP
Standard deviation of beta distribution for methylation level of CpG
loci. In range [0..1]. Default: 0.03.
.HP
\fB\-\-meth\-chg\-mu\fR DOUBLE
.IP
Median of beta distribution for methylation level of CHG loci. In
range [0..1]. Default: 0.08.
.HP
\fB\-\-meth\-chg\-sigma\fR DOUBLE
.IP
Standard deviation of beta distribution for methylation level of CHG
loci. In range [0..1]. Default: 0.008.
.HP
\fB\-\-meth\-chh\-mu\fR DOUBLE
.IP
Median of beta distribution for methylation level of CHH loci. In
range [0..1]. Default: 0.05.
.HP
\fB\-\-meth\-chh\-sigma\fR DOUBLE
.IP
Standard deviation of beta distribution for methylation level of CHH
loci. In range [0..1]. Default: 0.005.
.PP
VERSION
.IP
Last update:
mason_methylation version: 2.0.7 [tarball]
SeqAn version: 2.3.1