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Chromosome capture experiments, like Hi-C, typically bin the genome into distinct bins. A contact matrix, $M$, is given by $M_{i,j} = |\{pairs | mate_1 \in bin_i, mate_2 \in bin_j\}|$.

If one of the read mates spans a bin boundary, where should that pair be assigned?

For example, if $mate_1$ overlaps $bin_i$ and $mate_2$ overlaps both $bin_j$ and $bin_{j+1}$, should this read pair be assigned to $M_{i,j}$ or $M_{i,j+1}$? Should it be randomly assigned to either bin with equal probability? Should it be assigned to both?

I know this may be a rare event, but if Hi-C datasets are generated using billions of reads (such as Rao et al., Cell, 2014), this is bound to happen.

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