Fig. 4

The number of reproducible footprints scales with library depth. a CTCF footprints inferred from HEK293 ATAC-seq data (left) and DNase-seq data (right). Vertical lines depict the edges of the motif match. b Overlap between reproducible CTCF footprints in the HEK293 DNase-seq and combined ATAC-seq replicates, found using the FLR-IDR strategy. c Numbers of reproducible CTCF footprints in HEK293 ATAC-seq datasets at different depths. d The overlaps between one set of footprints in c shown for high vs. medium (left), high vs. low (middle), and medium vs. low sets (right). e The ratio of reproducible CTCF footprints (IDR footprints) or all CTCF motif regions with positive footprint scores (all footprints) that overlap CTCF ChIP-seq peaks, in all six individual sets at different depths (Additional file 1: Table S3). Red dashed line indicates this ratio for all considered CTCF motif sites