mason_methylation - Methylation Level Simulation
mason_methylation [OPTIONS] -i IN.fa
-o OUT.fa
Simulate methylation levels for IN.fa and write them to
OUT.fa.
- -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-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.