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Enhancer identification in mm10 from RRBS data in R

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

Kind Regards, Rahel

r rrbs enhancer mm10 visualization
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written by rahel14350 • rahel14350

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...

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written by ATpoint ATpoint

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

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written by rahel14350 • rahel14350

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?

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written by ATpoint ATpoint

1 answer

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

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written by rahel14350 • rahel14350

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