Metheor: Ultrafast DNA methylation heterogeneity calculation from bisulfite read alignments
Fig 1
(A) The input for Metheor is bisulfite read alignment tagged with Bismark methylation call strings. Using each of the seven subcommands shown, Metheor computes the corresponding DNA methylation heterogeneity measure. If reads were aligned with a tool other than Bismark, Metheor can still add tag for methylation call string with metheor tag subcommand to make alignment file compatible for Metheor run. (B) Schematic diagram for DNA methylation heterogeneity measures and benchmark settings in this study. [5] denote the Perl script provided by the authors along with the article proposing the utility of MHL. (C, D) Schematic diagram illustrating (C) read-centric algorithm and (D) CpG-centric algorithm for the computation of DNA methylation heterogeneity. The advantages (plus symbol) and disadvantages (minus symbol) are shown below the diagrams. (E) Distribution of the average number of CpGs per sequencing read for the RRBS data from 928 CCLE cell lines. (F) Genomewide average levels of proportion of discordant reads (PDR) and local pairwise methylation discordance (LPMD) against varying read lengths. (G) Schematic illustration for the definition of local pairwise methylation discordance (LPMD) and examples. The proportion of reads having different DNA methylation states for a pair of CpGs (red arrows) are computed.