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.


Your Answer

By clicking “Post Your Answer”, you agree to our terms of service, privacy policy and cookie policy

Browse other questions tagged or ask your own question.