Fig. 4: Comparison of CpG methylation predictions from nanopore with whole-genome bisulfite sequencing (WGBS).
From: Systematic benchmarking of tools for CpG methylation detection from nanopore sequencing
a Distribution of methylation calls (n = 1743) from nanopore (y axis) across three WGBS methylation bins: no or low methylation (0.0–0.3) (n = 793), intermediate methylation (0.3–0.7) (n = 264), and high or full methylation (0.7–1.0) (n = 686). In the boxplots, the lower and upper boundaries of the box are the first and third quartiles of the data, respectively, with the median indicated by a thick black line. The lower and upper whiskers extend to 1.5 times the interquartile range. The outliers are represented by the black dots. b Pearson’s correlation (r) (y axis) between methylation frequencies calculated from nanopore reads and WGBS at sites by each of the tested tools (combining predictions from both strands) at each level of minimal input coverage, i.e., minimum number of nanopore reads considered per site as reported from the BAM file (x axis). c Mean reported coverage (using the coverage reported by each tool for all sites) at each value of minimum input coverage in b. METEORE (RF) is the combination of Megalodon and DeepSignal using a random forest (parameters: max_depth = 3 and n_estimator = 10), and METEORE (REG) is the combination of Megalodon and DeepSignal using a regression model.
