We also learned independent 15-state models individually on each of the 127 epigenomes using the core set of 5 marks and the same parameter settings as for the primary model. In order to compare the individual models to the joint 15 state primary model, we stacked the emission vectors for all states from all the models and hierarchically clustered them using Euclidean distance and Ward linkage (Extended Data 2a). The individual epigenome models consistently and repeatedly identified states that were also recovered by the joint model (Extended Data 2a). Two additional clusters which included states recovered by the independent models learned in individual cell types, but not recovered in the joint model, were HetWk, characterized by weak presence of H3K9me3, and Rpts, characterized by presence of H3K9me3 along with a diversity of other marks, which was enriched in a large number of repeat elements.
