I have 2 timepoint-specific conditions (
t=X) and 12 specimens. I used nanopolish to calculate methylation signatures per base, in particular, with this script: https://github.com/jts/nanopolish/blob/master/scripts/calculate_methylation_frequency.py
The output generated looks like the following:
methylated_frequency ranges from floating point values within the range [0,1] (e.g. 0.0, 0.382, 0.618, 1.0)
Are there anyways I can use this data to calculate differential methylation between my groups?
For example, maybe methylation events in region
[x-y] are differentially methylated in
t=X compared to
t=0 or vice versa.