dmtools ebsrate

Description

For bisulfite sequencing data, the level of DNA methylation is estimated by converting unmethylated cytosine (C) to thymine (T) and then calculating the percentage of T at sites where the reference genome is C. The accuracy of this estimation depends on the bisulfite conversion rate, which directly affects the percentage of C to T. To evaluate the conversion rate of bisulfite, lambda sequences are typically added during library construction. The Lambda sequence is a completely unmethylated sequence, so after bisulfite treatment, all C sites should be converted to T with 100% efficiency.

However, some WGBS data do not include lambda sequences for estimating the conversion rate of bisulfite. In such cases, we can use several alternative methods to evaluate the conversion rate: (1) calculating the mitochondrial methylation level (applicable to some mammals); (2) calculating the DNA methylation level of CHH (applicable to some animals); (3) calculating the methylation level of a specific chromosome specified by the user; and (4) calculating the methylation level of chloroplasts (applicable to some plants). It is important to note that some studies have reported DNA methylation in mitochondria, so using mitochondrial DNA methylation level to estimate the conversion rate of bisulfite requires careful consideration.

You can estimate the bisulfite conversion rate with dmtools:

Usage

CHH mode

$ dmtools ebsrate -i mutant.methratio.dm --bsmode chh
  #dm bs-c-rate
  ###bs rate calculated by chh
  #ebsrate chh mode
  #CHH      chrM    0.004437
  #CHH      chr1    0.004765
  #CHH      chr2    0.004755
  #...
  #...
  #CHH      chrX    0.004585
  ###CHH level in all chromosome
  #CHH      +       0.004752
  #CHH      -       0.004714
  #CHH      .       0.004733
  ###estimated bs rate by CHH level in all chromosome
  #bsrate   0.004733

chrM mode

$ dmtools ebsrate -i GSM1329865.zm0.dm --bsmode chrM
  #dm bs-c-rate
  ###bs rate calculated by chrM
  #ebsrate chr mode
  #Chromosome List chrM 16569
  #chrM     0       16569   0.005053        C       +
  #chrM     0       16569   0.005588        CG      +
  #chrM     0       16569   0.005007        CHG     +
  #chrM     0       16569   0.005001        CHH     +
  #chrM     0       16569   0.004336        C       -
  #chrM     0       16569   0.006145        CG      -
  #chrM     0       16569   0.003907        CHG     -
  #chrM     0       16569   0.003873        CHH     -
  ###estimated bs rate by chrM level
  #bsrate   0.004694

lambda DNA mode

$ dmtools ebsrate -i GSM1329865.zm0.dm --bsmode lambda
  ###estimated bs rate by lambda level
  #bsrate   0.01092

Parameters

-i input DM file

-o output file

--bsmode chh or chr mode, suggest chh for human, mouse etc.

--chr chromosome used for calculate bisulfite convertion rate, default, chrM and chrC

Tip

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