Fig. 2

Sample output from ChromTime with contracting peaks. Genome browser screenshot with sample output of ChromTime for H3K4me2 from the T-cell development time course in mouse [17] with five time points at the Esam/Vsig2/Nrgn locus. Time points 1, 2, and 3 correspond to in vitro differentiated T-cell precursors (FLDN1, FLDN2a, and FLDN2b), whereas time points 4 and 5 correspond to in vivo purified thymocytes (ThyDN3 and ThyDP). The input ChIP-seq signal and MACS2 [38] peaks (black boxes under each signal track) are shown in the upper panel of the screenshot. The ChromTime-predicted peaks colored by their boundary dynamics for each block at each time point are shown in the bottom panel. The first peak in each block is colored in dark gray. Each subsequent peak is colored with respect to the predicted dynamic relative to its previous time point. Peaks with steady boundaries on both sides are shown in light gray, and those with at least one contracting boundary are shown in blue. Nearby peaks that touch boundaries are visualized as one peak by the genome browser. Not shown in the figure are expanding peaks, peaks at single time points, and peaks with opposite dynamics (EXPAND on the left and CONTRACT on the right, or vice versa), which would be colored in red, orange, and black, respectively. See Additional file 1: Figure S2 for examples of predicted expanding peaks