Question: How to quantify the DNA methylation level of a gene from WGBS data?
0
gravatar for wangzer
10 months ago by
wangzer0
wangzer0 wrote:

I have got the WGBS data and the methylation the ratio of the all sites. But I want to know the every genes' methylation level. How to quantify the DNA methylation level of a gene from WGBS data? Finally, I want plot a fig. like this. What tools can I use to implement it?enter image description here

dna methylation tool quantify R • 330 views
ADD COMMENTlink modified 10 months ago by Devon Ryan92k • written 10 months ago by wangzer0
1
gravatar for Devon Ryan
10 months ago by
Devon Ryan92k
Freiburg, Germany
Devon Ryan92k wrote:

Genes don't really have a methylation level, what you're plotting is the average of the CpG methyation in a gene. So load your data, calculate that and then plot it. You can do all of that in R (probably with GenomicRanges to make life easier).

ADD COMMENTlink written 10 months ago by Devon Ryan92k

thanks,I will try again.

ADD REPLYlink written 10 months ago by wangzer0
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