Fig. 3

scATAC-seq reads outside of peaks or within repeat regions improve cell grouping. a-d Local grouping. The distribution for all K562 cells of the number of cells among each cell’s 20 nearest neighbors that share its sample label (x axis). P-values: Wilcoxon rank sum test. e-h Global grouping. ROC curves for how well cells within the same sample are distinguished from those in different samples by their distance in significant PC space. P-values calculated by bootstrapping (Methods). (a, e) reads in (red) vs. outside (blue) of peaks called on pooled scATAC data for K562 s; (b, f) reads in (red) vs. outside (blue) of peaks called on high-coverage K562 DNaseI-seq, considering only untreated K562 cells; (c, g) all reads (red) vs. only reads outside repeat elements (blue); or (d, h) using gapped (red) or ungapped (blue) k-mers