# Where to assign a read pair when a mate spans a HiC bin boundary?

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.