I am looking to identify differences in methylation between two isogenic replicates of E coli. I have oxford nanopore sequencing of three biological replicates for two strains, and am looking to compare methylation between them.
I have done nanopolish analysis and visualized the methylation frequency using ggplot2 in R, and have found no differences in the CpG methylation.
Are there any tools I could use to definitively compare methylation between two strains? Ideally this would generate a PCA plot showing distinct/overlapping methylation profiles.
Thank you for any advice!