Question: Calculating bisulfite conversion rates?
gravatar for dakterl79
3.3 years ago by
dakterl7920 wrote:


I am trying to calculate the bisulfite conversion rates for whole genome bisulfite sequencing dataset.

The bisulfite conversion rate of each base (non-CpG) can be calculated as T / (T + C) * 100, where T is thymine and C is cytosine read numbers on that base.

Below is from the aligned (by bismark) and methylation-called (by methylKit) file of one sample (CHH context).

chrBase chr base strand coverage freqC freqT

scaffold1.1005 scaffold1 1005 F 12 0.00 100.00

scaffold1.1006 scaffold1 1006 F 13 0.00 100.0

scaffold1.1016 scaffold1 1016 F 17 0.00 100.00

scaffold1.1024 scaffold1 1024 F 18 0.00 100.00


To calculate overall conversion rate of this sample, i think i should calculate below. 1. all C = sum of (freqC * coverage) in this sample 2. all T = sum of (freqT * coverage) in this sample 3. overall conversion rate = all T / (all C + all T)

Is it correct?

Also, what is the acceptable range of non-conversion rates?

Thank you very much!

wgbs methylome • 1.4k views
ADD COMMENTlink modified 3.3 years ago • written 3.3 years ago by dakterl7920
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 2372 users visited in the last hour