Fig. 2: True CTCF binding sites have a bimodal strand-specific distribution centered on the CTCF motif.

A Unfiltered reads +/− 1250 bp around a CTCF binding site located on the negative strand (chr1: 30,779,763 − 30,779,781). The midpoint of the CTCF motif is marked with the symbol “ <”, representing that it is on the negative strand, and a pink line. B Plot (A) filtered to observed ligations (equivalently, short fragments.) C Schematic demonstrating the bimodal read pile-up around a CTCF binding site. Created in BioRender. Aryee, M. (2025) https://BioRender.com/g98u240 (D) Plot (B) as a density plot and zoomed in on the CTCF motif, with quadrant annotations. E Distributions of reads in quadrants for true negative and true positive CTCF binding sites in DNA loop anchors. True positives are defined as CTCF motifs that are the only CTCF motif in a loop anchor and within 30 bp of a CTCF ChIP-seq peak. True negatives are areas of the loop anchors with one CTCF motif that are at least 200 bp from the CTCF motif. 3,984,150 fragments across 4523 loop anchors each containing one CTCF binding site are used to make these boxplots. Boxplots are made with ggplot2::geom_boxplot() and show the 25% quantile (lower bound of box), median (center line), and 75% quantile (upper bound of box). Boxplot whiskers subtract (lower whisker) or add (upper whisker) 1.5 * IQR from the lower bound (lower whisker) or upper bound (upper whisker) of the box. Schematics of the quadrant read pile-up patterns are shown next to the corresponding true positive and true negative boxplots. F CAMEL statistic \((\hat{\alpha }=\frac{\min ({n}_{2},{n}_{4})}{\max ({n}_{1},{n}_{3})})\) for plot (D) peaks at the CTCF motif.