Fig. 3

SeATAC recovers nucleosome positions from sparse ATAC-seq. a The ROC curve for recovering nucleosome positions from ATAC-seq with 0.1%, 1%, and 10% of the sequencing reads randomly sampled from the full dataset (GM12878). b The heatmaps shows the nucleosome density estimated by SeATAC (blue) and NucleoATAC (purple) on a 1% down-sampled dataset. There are 2042 and 3453 regions (640 bp) identified by both SeATAC/NucleoATAC and by SeATAC only as nucleosomes. The NucleoATAC signal on the full dataset (black) and a MNase-seq dataset on GM12878 (red) for these regions are also shown. c 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. d The AUC of SeATAC and NucleoATAC at different read counts cutoff from 1 to 20 (the minimum reads in a V-plot)