How does call-methylation work?

isnmn commented 9 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 9 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 9 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 9 months ago

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

jts / nanopolish

How does call-methylation work? #1120