Question: Low methylation regions or non-methylation regions from WGBS dataset
1
gravatar for Shicheng Guo
3.3 years ago by
Shicheng Guo7.5k
Shicheng Guo7.5k wrote:

Hi All,

Any method or software to recommend to identify low methylation regions or non-methylation regions from WGBS dataset?

  1. swDMR
  2. MethylSeekR

Thanks. 

methylation • 1.0k views
ADD COMMENTlink modified 9 months ago • written 3.3 years ago by Shicheng Guo7.5k
3
gravatar for Devon Ryan
3.3 years ago by
Devon Ryan90k
Freiburg, Germany
Devon Ryan90k wrote:

MethylSeekR from Bioconductor

ADD COMMENTlink written 3.3 years ago by Devon Ryan90k
1
gravatar for Antonio R. Franco
3.3 years ago by
Spain. Universidad de Córdoba
Antonio R. Franco4.0k wrote:

Any recommendation for plant methylation? (CHH and CHG methylation are also involved)

ADD COMMENTlink written 3.3 years ago by Antonio R. Franco4.0k
1

I would still try MethylSeekR there as well. If it starts demanding CpGs then one can probably just lie to it and still get the correct results (maybe try a little test dataset first).

ADD REPLYlink written 3.3 years ago by Devon Ryan90k
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