I have methylation data from ONT sequencing expressed as percentage of methylation and/or number of reads. I don't know if I'm supposed to normalize the data and how to handle replicates. Some ideas: I have data in triplicate. I want to normalize the data (quantile normalization is the preferred option) and/or collapse data to have 1 file/dataset from 3 replicates (doing weighted average maybe). So 1 idea would be just to perform a weighted average of each methylation value doing [%M*NR] where %M is the percentage of methylated reads and NR is the number of reads, per each methylated position. In this case I will lose the meaning of the percentage value in the downstream analyses because I will have a weighted value. Otherwise, I can perform quantile normalization on the number of reads (total and methylated) and then calculate the percentage of methylated reads. I would like the opinion of someone with a better statistical background than me ;) thanks for your kind help!

       %M-S1  NR-S1 %M-S2  NR-S2 %M-S3  NR-S3
Meth1   20     60     15     54    41     12
Meth2   40     14     78     52    13     65
Meth3   12     94     73     19    37     70
Meth4   36     77     69     14    26     74