How does call-methylation work?

isnmn commented 11 months ago

Hi, I may missed that in the documentation but I have several questions about how call-methylation pipeline works:

Does nanopolish use some sort of background noise to calculate methylation frequency?
How are log_lik_meth or _demeth calculated? What type of data or information is used for this calculation?
For example if log_lik_ratio is 1 does that mean the methylation in that region is equal to the background noise? Or is it equal to genome-wide methylation frequency?

Could you please elaborate more? I couldn't find detailed information about these and without knowing it's not scientifically correct or easy to interpret the results.

jts commented 11 months ago

Hi,

Please see our paper describing the method, which describes the procedure in detail: https://www.nature.com/articles/nmeth.4184

Jared

isnmn commented 10 months ago

so can you correct me if i'm wrong? as far as i understood, the log_lik_ratio > 0 means methylation but does log_lik_ratio < 0 means demethylation or no methylation changes at all?

jts commented 10 months ago

< 0 means that the signal looks more like the canonical (C, not methylated) base

jts / nanopolish

How does call-methylation work? #1120