Extended Data Fig. 6. Profiles of peak calls generated by different peak callers for various assays.

a, Aggregated profiles of epigenomic marks, transcription binding sites, and chromatin accessibility in true enhancer regions and distal TREs identified by different peak callers for TSS- and NT-assays. The shaded area indicates the 95% confidence interval of mean values estimated via bootstrap; b, An example demonstrating why MACS2 is not suitable for identifying TREs. c, Distribution of element sizes identified from 12 assays by all applicable peak callers. In the box plot, the center lines, box limits, and whiskers denote the median, upper and lower quartiles, and 1.5× interquartile range, respectively; points show observations that are not in the range of quartiles $\pm 1.5\times {(Q}_3-Q_1)$. A table of sample sizes is available in Supplementary Table 5.