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MASON_METHYLATION(1) MASON_METHYLATION(1)

NAME

mason_methylation - Methylation Level Simulation

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
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: .sam[.*], .raw[.*], .gbk[.*], .frn[.*], .fq[.*], .fna[.*], .ffn[.*], .fastq[.*], .fasta[.*], .faa[.*], .fa[.*], .embl[.*], and .bam, where * is any of the following extensions: gz, bz2, and bgzf for transparent (de)compression.
-o, --out INPUT_FILE
Input FASTA file with genome. Valid filetypes are: .sam[.*], .raw[.*], .frn[.*], .fq[.*], .fna[.*], .ffn[.*], .fastq[.*], .fasta[.*], .faa[.*], .fa[.*], and .bam, where * is any of the following extensions: gz, bz2, and bgzf for transparent (de)compression.

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.
mason_methylation 2.0.8 [tarball]