Differential calling and reproducibility in H3K4me3 ChIP-Seq data sets. A-C MMD-based distances as a function of mean total counts in experiment AB.1. Each dot represents one examined promoter. A MMD values computed between Cfp1-/- and WT. B MMD determined between Resc and WT overlayed in black. These provide a measure of the biological and experimental variability. C Plots are overlayed and promoters that are significantly different in Cfp1-/- versus WT/Resc (FDR < 0.05) are shown in red. D-E MA plot representations of the same data showing smooth scatter plots of log2 fold changes versus mean normalised counts. The red dots mark promoters detected as differentially modified (DMPs) at a 5% false discovery rate. D DMPs according to MMDiff and E according to DESeq. F Reproducibility of differential calling across experiments AB.1 and AB.2. DESeq and MMDiff are compared both for differentially called promoters (left) and for MACS consensus peaks.