Fig. 2.

Overview of the counting strategy with bin pairs. The linear genome is partitioned into bins of constant size, such that the interaction space is partitioned into bin pairs (boxes). Read pairs are shown as open circles and are distributed across the interaction space according to the mapping locations of both reads. For example, the marked read pair (closed circle) has one read on each of chromosomes A and B, mapped to the indicated location on each axis. The number of read pairs in each box is used as the count for the corresponding bin pair