Extended Data Fig. 2: RCMC more deeply and efficiently maps target loci than Hi-C.

(a) Interaction probability curves comparing the interaction frequency at different genomic separations (s) for the five M-to-G1 conditions, shown for RCMC on the left and Hi-C¹⁸ on the right. The first derivative of these P(s) curves is shown at the bottom. (b) Benchmarking comparison of RCMC’s ability to fill out high-resolution contact matrices against Hi-C¹⁸. Region-averaged calculations are shown for both methods across the M-to-G1 datasets. The x-axis shows the contact distance in bp, and the y-axis shows the fraction of all bins at a given contact distance within the captured locus that contain at least one read at 250 bp resolution. (c) As in (b), benchmarking comparison of successively downsampled RCMC’s ability to fill out high-resolution contact matrices against Hi-C for the ana/telophase condition. Downsampling was applied to all mapped ligated read pairs in increasing powers of 2 until (1/2)¹⁰, or 1/1024^th, of the initial dataset. (d) Contact map comparisons of successively downsampled RCMC data, starting from the full dataset (topmost) down to 1/1024^th (bottom) and with a comparison against the Hi-C dataset. Maps are shown for the Klf1 locus at 1 kb resolution in the ana/telophase condition on the left and for the Dag1 locus at 3.2 kb resolution in the late G1 condition on the right.