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.