.TH MASON_METHYLATION 1 "" "mason_methylation 2.0.9 [tarball]" ""
.SH NAME
mason_methylation \- Methylation Level Simulation
.SH SYNOPSIS
\fBmason_methylation\fP [OPTIONS] \fB-i\fP \fIIN.fa\fP \fB-o\fP \fIOUT.fa\fP
.SH DESCRIPTION
Simulate methylation levels for \fIIN.fa\fP and write them to \fIOUT.fa\fP.
.SH OPTIONS
.TP
\fB-h\fP, \fB--help\fP
Display the help message.
.TP
\fB--version\fP
Display version information.
.TP
\fB-q\fP, \fB--quiet\fP
Low verbosity.
.TP
\fB-v\fP, \fB--verbose\fP
Higher verbosity.
.TP
\fB-vv\fP, \fB--very-verbose\fP
Highest verbosity.
.TP
\fB--seed\fP \fIINTEGER\fP
Seed for RNG. Default: \fI0\fP.
.TP
\fB-i\fP, \fB--in\fP \fIINPUT_FILE\fP
Input FASTA file with genome. Valid filetypes are: \fI.sam[.*]\fP, \fI.raw[.*]\fP, \fI.gbk[.*]\fP, \fI.frn[.*]\fP, \fI.fq[.*]\fP, \fI.fna[.*]\fP, \fI.ffn[.*]\fP, \fI.fastq[.*]\fP, \fI.fasta[.*]\fP, \fI.faa[.*]\fP, \fI.fa[.*]\fP, \fI.embl[.*]\fP, and \fI.bam\fP, where * is any of the following extensions: \fIgz\fP, \fIbz2\fP, and \fIbgzf\fP for transparent (de)compression.
.TP
\fB-o\fP, \fB--out\fP \fIINPUT_FILE\fP
Input FASTA file with genome. Valid filetypes are: \fI.sam[.*]\fP, \fI.raw[.*]\fP, \fI.frn[.*]\fP, \fI.fq[.*]\fP, \fI.fna[.*]\fP, \fI.ffn[.*]\fP, \fI.fastq[.*]\fP, \fI.fasta[.*]\fP, \fI.faa[.*]\fP, \fI.fa[.*]\fP, and \fI.bam\fP, where * is any of the following extensions: \fIgz\fP, \fIbz2\fP, and \fIbgzf\fP for transparent (de)compression.
.SS Methylation Level Simulation:
.TP
\fB--methylation-levels\fP
Enable methylation level simulation.
.TP
\fB--meth-cg-mu\fP \fIDOUBLE\fP
Median of beta distribution for methylation level of CpG loci. In range [0..1]. Default: \fI0.6\fP.
.TP
\fB--meth-cg-sigma\fP \fIDOUBLE\fP
Standard deviation of beta distribution for methylation level of CpG loci. In range [0..1]. Default: \fI0.03\fP.
.TP
\fB--meth-chg-mu\fP \fIDOUBLE\fP
Median of beta distribution for methylation level of CHG loci. In range [0..1]. Default: \fI0.08\fP.
.TP
\fB--meth-chg-sigma\fP \fIDOUBLE\fP
Standard deviation of beta distribution for methylation level of CHG loci. In range [0..1]. Default: \fI0.008\fP.
.TP
\fB--meth-chh-mu\fP \fIDOUBLE\fP
Median of beta distribution for methylation level of CHH loci. In range [0..1]. Default: \fI0.05\fP.
.TP
\fB--meth-chh-sigma\fP \fIDOUBLE\fP
Standard deviation of beta distribution for methylation level of CHH loci. In range [0..1]. Default: \fI0.005\fP.