Low methylation regions or non-methylation regions from WGBS dataset

Question

[Shicheng Guo]

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

Answer 1

[Devon Ryan]

MethylSeekR from Bioconductor

Answer 2

[Antonio R. Franco]

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

[Devon Ryan]

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).