Enhancer identification in mm10 from RRBS data in R

Question

[rahel14350]

Dear all, Do you know any R packages that I can identify and visualize the enhancers from RRBS data in mm10?

Kind Regards, Rahel

[ATpoint]

There is in my opinion no reliable method to identify enhancer elements only based on methylation data since methylation is not specific to enhancers. Enhancers are regulatory elements that boost / regulate transcription. methylation is simply an epigenetic modification, nothing more. It indeed regulates enhancers but this is not an enhancer-exclusive feature. You find DNA methylation also on promoters, gene bodies, laminar-associated domains etcetcetc...

[rahel14350]

Many thanks for your reply. Then any tools like ngs.plot/compEPiTools are not useful in the case of RRBS data?

[ATpoint]

That is not what I am saying. I only said that RRBS alone is not a reliable method to identify enhancers. What exactly do you want to do?

Answer 1

[rahel14350]

Deeptools based on region-scale helped me a lot. https://deeptools.readthedocs.io/en/develop/content/tools/plotProfile.html