Man page - mason_methylation(1)

Packages contains this manual

Package:  seqan-apps
apt-get install seqan-apps

Manuals in package:
• rabema_evaluate(1)
• alf(1)
• mason_materializer(1)
• pair_align(1)
• gustaf(1)
• stellar(1)
• razers3(1)
• sak(1)
• yara_indexer(1)
• mason_frag_sequencing(1)
• micro_razers(1)
• rabema_prepare_sam(1)
• insegt(1)
• rabema_build_gold_standard(1)
• splazers(1)
• seqan_tcoffee(1)
• yara_mapper(1)
• tree_recon(1)
• mason_genome(1)
• mason_methylation(1)
• razers(1)
• snp_store(1)
Documentations in package:
• seqan-apps

Manual

MASON_METHYLATION

NAME
SYNOPSIS
DESCRIPTION
OPTIONS
Methylation Level Simulation:

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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 .

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