Irreproducibility Discovery Rate (IDR) assays to compare peak calling algorithms. (A) IDR assay comparing biological replicate datasets (see text for details). Note that for H3K4me3, MeDiChISeq continues to find significant common events in compared replicate datasets with slowly increasing IDR while the IDRs sharply increase for the three other peak callers around 5,000 significant peaks commonly identified in the replicates. (B) Similar reproducibility analysis but performed by pairwise comparison of binding site predictions by the different peak callers indicated at the left (“virtual replicates”). This approach reflects the concordance in binding site identification between two peak callers. Note that in all illustrated IDR assays, MeDiChISeq predictions have the lowest IDR levels for the highest number of significant binding sites. In (A) and (B) dashed lines indicate IDR levels of 0.1; i.e. a reproducibility level of 90%.