mason_methylation1
Methylation level simulation
Usage
mason_methylation [OPTIONS]
-i
IN.fa
-o
OUT.fa
Overview
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.
Releases
5 releases since Debian 9 (Stretch); the text changed 1 time.
--help since Debian 10 (Buster);
--in since Debian 10 (Buster);
--meth-cg-mu since Debian 10 (Buster);
--meth-cg-sigma since Debian 10 (Buster);
--meth-chg-mu since Debian 10 (Buster);
--meth-chg-sigma since Debian 10 (Buster);
--meth-chh-mu since Debian 10 (Buster);
--meth-chh-sigma since Debian 10 (Buster);
--methylation-levels since Debian 10 (Buster);
--out since Debian 10 (Buster);
--quiet since Debian 10 (Buster);
--seed since Debian 10 (Buster);
--verbose since Debian 10 (Buster);
--version since Debian 10 (Buster);
--very-verbose since Debian 10 (Buster);
-h since Debian 10 (Buster);
-i since Debian 10 (Buster);
-o since Debian 10 (Buster);
-q since Debian 10 (Buster);
-v since Debian 10 (Buster);
-vv since Debian 10 (Buster).