Question: From WGBS-seq to DMR calling and annotation
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gravatar for zhengyunchaosky
2.4 years ago by
Technical University of Munich
zhengyunchaosky20 wrote:

Hi, friends, I am new in Whole Genome Bisulfite Sequencing (WGBS-seq) analysis. About Differentially Methylated Regions (DMRs) calling, I have read some papers directly using Fisher Test to detect DMRs and there are also some R packages built to do the detection. Do you have any advice on DMR calling? Also for the annotation (genes, transposable elements), any advice on carrying out the annotation? Thanks so much in advance!

sequencing R • 1.7k views
ADD COMMENTlink modified 2.4 years ago • written 2.4 years ago by zhengyunchaosky20
1

For DMR calling, you could use (among many packages) methylKit. It has a solid documentation, is actively being maintained, authors respond to issues on Github, and has the option to aggregate CpG counts over user-specified regions in order to call DMRs. Once you have the DMRs, you could use (again among many) annotatR.

ADD REPLYlink written 2.4 years ago by ATpoint40k

Great! Thank you so much for your advice!

ADD REPLYlink written 2.4 years ago by zhengyunchaosky20

You're very welcome.

ADD REPLYlink written 2.4 years ago by ATpoint40k
0
gravatar for zhengyunchaosky
2.4 years ago by
Technical University of Munich
zhengyunchaosky20 wrote:

Great! Thank you so much for your advice!

ADD COMMENTlink written 2.4 years ago by zhengyunchaosky20
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