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smithlabcode / methpipe

A pipeline for analyzing DNA methylation data from bisulfite sequencing.
http://smithlabresearch.org/methpipe
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average 5hmC and true 5mC level in regions of interest? #190

Closed BenvanderVeer closed 2 years ago

BenvanderVeer commented 2 years ago

Dear Methpipe Authors,

I have both oxBS and BS data and I estimated 5hmC and true 5mC levels using the MLML program.

I was wondering what the best way would be to calculate the 5hmC and 5mC levels over specific regions of interest (e.g. LINE elements, or promotors)? Should this be a weighted average by taking the total coverage of both oxBS + BS for each individual CpG, or average the methylation level of the individual CpGs? Or is there even another preferred method for this, or maybe it is not possible?

best, Ben

andrewdavidsmith commented 2 years ago

@BenvanderVeer I'm very happy to answer this question -- or at least give my personal opinion on it. But since this is somewhat outside technical details of the software development, it would be best if you contacted me directly by email.

BenvanderVeer commented 2 years ago

Thank you, I send an email this morning!