table of contents
| 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 2.0.9 [tarball] |