Fig. 1

Rationale behind Cluster-Based analysis of CpG methylation (CluBCpG). a Each WGBS read originates from a DNA molecule within a single cell (filled and empty circles in tanghulu plots represent methylated and unmethylated CpG sites; columns and rows represent CpG sites and WGBS reads, respectively). The dotted-outline box represents a tissue sample, and colored shapes represent different cell types. Conventionally, methylation is measured by averaging methylated and unmethylated reads at each CpG site. Instead, CluBCpG groups reads based on methylation patterns. (Note: By default, 4 reads of identical methylation pattern are required to comprise a cluster; single-read “clusters” are depicted here for simplicity.) b Conceptually, CluBCpG can be utilized to compare two samples (dotted boxes) to find cell type-specific differences by identifying patterns that are unique to one of the input samples