Fig. 4

Platform CpG-unit region coverage and CpG-unit overlap. a Number of CpG-units identified in targeted and off-target regions by each platform. WGBS-PBAT (orange) covers ~ 14.4 M CpG-units; however, there is no notion of targeted regions in this platform. The targeted platforms predicted total CpG-units are depicted as gray bar and coverage of the CpG-units in the predicted regions (on-target) are shown in blue. CpG-units outside the predicted set (off-target) are shown in red bars. b Barplot of the percent recovery of targeted CpG-units. c Density plots showing the portion of the regions covered by the data where the y-axis is the length of the region from 0 to 100% and the color scale is fraction of CpG-units covering a location of the region. Primarily the end of the region is covered by all methods, however ERRBS shows abundant coverage in the start of the region and to a lesser degree throughout the region. These plots demonstrate that the reduced number of recovered CpG-units in ERRBS relative to the other platforms is attributed to increased number of missed CpG-units shown as increased density at 0% region. d Overlap of CpG-units across the four platforms. The UpSet visualization technique [43] for set intersections is displayed as matrix layout. Horizontal bars on the lower left indicate the total number of annotated CpG-units in the set. Dark circles in the matrix (lower right) indicate sets that are part of the intersection. Bars in the main plot area (upper right) indicate the number of intersecting CpG-units for the sets represented by the dark circles