dmtools chrmeth

Description

DMtools can calculate cytosine methylation level of one chromosome.

To calculate the methylation density level of one chromosome, only cytosines with coverage greater than the preset threshold are used. The DNA methylation level in this chromosome is defined as the total number of sequenced Cs over the total number of sequenced Cs and Ts at all cytosine positions across this chromosome, and the equation is as follows:

\[\begin{split}ML(x)_{method} = \begin{cases} \dfrac{\sum_{i=1}^{N} C}{\sum_{i=1}^{N} (C + T)}, & \text{if method = weighted} \\ \dfrac{\sum_{i=1}^{N} ML(x_{i})}{N}, & \text{if method = mean} \\ \end{cases}\end{split}\]

where N is the total number of cytosine sites whose coverage is more than the predefined threshold in the chromosome.

Usage

Calculate DNA methylation level of one chromosome:

$ dmtools chrmeth -i sample1.methratio.dm -o chromosome.chr1me.txt \
  --chr chr1
#chr1       0       248956422       0.019026        C       +
#chr1       0       248956422       0.303933        CG      +
#chr1       0       248956422       0.004569        CHG     +
#chr1       0       248956422       0.004762        CHH     +
#chr1       0       248956422       0.018981        C       -
#chr1       0       248956422       0.303064        CG      -
#chr1       0       248956422       0.004570        CHG     -
#chr1       0       248956422       0.004769        CHH     -

Please see 'dmtools chrmeth' for more details.

Parameters

-i input DM file

-o output file

--chr chromosome for cal.

Tip

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