The relative representation of cis-regulatory elements genome-wide by different DNA methylation assays. We use the ATAC-seq peaks as a representation of the cis-regulatory elements in GM12878 cells. These were further subdivided into those distal (>10 kb upstream or >2 kb downstream) from RefSeq genes. The X-WGBS results interrogate at least one CG in the majority of these loci at 5 or 10× coverage, whereas RRBS represents only a small proportion of these loci, with the Infinium HumanMethylation450 microarray and the SeqCap Epi CpGiant system representing similar proportions (as expected for designs targeting the same genomic loci), with the expanded Infinium MethylationEPIC microarray representing a higher proportion of ATAC-seq peaks.
