Calmeth.rst

Calculate DNA methylation level

Calmeth

Calculate DNA methylation level from alignment files, you can obtained single-base cytosine DNA methylation results, and the chromosome region DNA methylation levels files.

An example usage is:
  with bam file:
    calmeth [options] -g genome.fa  -b alignment.sort.bam -m output.methrario.txt
  with sam file:
    calmeth [options] -g genome.fa  -i alignment.sort.sam -m output.methrario.txt

Important

The bam or sam file MUST sorted by samtools sort.

Paramaters

**[ Main paramaters ]	**
-m/--methratio	[MethFileNamePrefix] Predix of methratio output file
--genome/-g	Name of the genome mapped against, MUST build index first bdindex
-i/--input	Sam format file, sorted by samtools sort.
-b/--binput	Bam format file, sorted by samtools sort.
-Q [int]	caculate the methratio while read QulityScore >= Q. default:20
-n [float]	Number of mismatches, default 0.06 percentage of read length. [0-1]
-c|--coverage	>= <INT> coverage. default:4
-nC	>= <INT> Cs per region. default:1
-R/--Regions	Bins for DMR caculate , default 1000(1kb) .
--binsfile
|DNA methylation l	evel distributions in chrosome, default output file: {Prefix}.methBins.txt
-s/--step
Chrosome using a default step: 50	n overlapping sliding window of 100000bp at a step of 50000bp. 000(bp)
-r/--remove_dup	REMOVE_DUP, default:true
-f|--sam [outfile]
f for sam format	outfile contain methState.
--sam-seq-beforeBS	Converting BS read to the genome sequences.
--help/-h	Print help

Output files

1. prefix.methratio.txt
2. prefix.methBins.txt
3. prefix_Region.CG/CHG/CHH.txt
4. prefix.mCdensity.txt
5. prefix.mCcatero.txt

Output file format

1. methratio
    Chromosome Loci Strand Context C_count CT_count methlevel eff_CT_count rev_G_count rev_GA_count MethContext 5context
    # ex. Chr1    61      +       CHH     3       11      0.286364        10.5    20      21      hU      ATCTT
    # C_count      The number of C in this base pair.
    # CT_count     The number of coverage in this base pair.
    # eff_CT_count Adjust read coverage based on opposite strand.
    # rev_G_count  The number of G in the reverse strand.
    # rev_GA_count The number of coverage in the reverse strand.
    # MethContext  M/Mh/H/hU/U, M means the methylation level ≥ 80%, etc
2. methBins
    Chrom BinIndex methlevel context
    # ex. Chr1    1       0.113674        CG
    # The BinIndex is defined by -s paramater in calmeth.
    # This file can be used for visualization the DNA methylation level acorss the chromosome.
3. Region
    chrom regionStart strand context c_count ct_count
    # ex. Chr1    1001    +       CG      1       227
    # The bins methylation level output file (BS.mr_Region.C*.txt) can be used to do DMR detection.
4. mCdensity
    CG/CHG/CHH C count in [0, 1%) [1%, 2%) ... [49%, 50%) ... [99%, 100%]
    # According to the DNA methylation level, the number of cytosine sites at different methylation levels was counted from 0 to 100.
5. mCcatero
    Average DNA methylation level including mC, mCG and other states.

Tip

For feature requests or bug reports please open an issue on github.