CpGs with a minimum read coverage of 5 were used to calculate the average methylation percentages within genomic regions labeled with each chromatin state from the 15 state primary model. Only regions containing more than 3 CpGs with at most 200bp between consecutive CpGs were used. Plots were generated using ggplot2 package for R (v.3.02). The average methylation levels for the chromatin states across DNA methylation platforms (WGBS, RRBS and mCRF) were analyzed using Standard Least Square models in JMP (v.11.0; SAS Ins.). The model included the platforms (3 levels), chromatin states (15 levels) and the interactions (Extended Data 4).
