NAME¶

SYNOPSIS

mason_methylation [OPTIONS] -i IN.fa -o OUT.fa

DESCRIPTION

Simulate methylation levels for IN.fa and write them to OUT.fa.

OPTIONS

-h, --help

Display the help message.

--version-check BOOL

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.

--version

Display version information.

-q, --quiet

Low verbosity.

-v, --verbose

Higher verbosity.

-vv, --very-verbose

Highest verbosity.

--seed INTEGER

Seed for RNG. Default: 0.

-i, --in INPUT_FILE

Input FASTA file with genome. Valid filetypes are: .fasta and .fa.

-o, --out INPUT_FILE

Input FASTA file with genome. Valid filetypes are: .fasta and .fa.

Methylation Level Simulation:

--methylation-levels

Enable methylation level simulation.

--meth-cg-mu DOUBLE

Median of beta distribution for methylation level of CpG loci. In range [0..1]. Default: 0.6.

--meth-cg-sigma DOUBLE

Standard deviation of beta distribution for methylation level of CpG loci. In range [0..1]. Default: 0.03.

--meth-chg-mu DOUBLE

Median of beta distribution for methylation level of CHG loci. In range [0..1]. Default: 0.08.

--meth-chg-sigma DOUBLE

Standard deviation of beta distribution for methylation level of CHG loci. In range [0..1]. Default: 0.008.

--meth-chh-mu DOUBLE

Median of beta distribution for methylation level of CHH loci. In range [0..1]. Default: 0.05.

--meth-chh-sigma DOUBLE

Standard deviation of beta distribution for methylation level of CHH loci. In range [0..1]. Default: 0.005.

VERSION

Last update: mason_methylation version: 2.0.7 [tarball] SeqAn version: 2.3.1