Fig. 4

SeATAC detects nucleosome changes. a The ROC curve for detecting nucleosome changes from ATAC-seq with 10% of the sequencing reads from the full dataset (GM12878). b The raw and estimated V-plot of a NFR (chr1:113,162,059–113,162,698) and a NOR (chr2:226,653,061–226,653,700) region are shown. The heatmap color indicates the normalized read density. c The heatmaps show the nucleosome density of ~ 5000 sampled NOR and NFR regions estimated by SeATAC (blue) and NucleoATAC (purple) on a 10% down-sampled dataset. There are 3276, 1278, 739, and 311 regions that are identified as a change from NFR to NOR (with decreased chromatin accessibility) by both SeATAC and NucleoATAC (11), by SeATAC only (10), by NucleoATAC only (01), and by neither of them (00), respectively. The NucleoATAC signal on the full dataset (black) and a MNase-seq dataset on GM12878 (red) for these regions are also shown. d The violin plot shows the AUC (area under ROC) of SeATAC and NucleoATAC on 523 ATAC-seq samples from 20 studies. ***Wilcoxon rank sum test p-value < 0.001. e The AUC of SeATAC and NucleoATAC at different read counts cutoff from 1 to 20 (the minimum reads in a V-plot)