Advances in computational ChIA‐PET data analysis

Genome‐wide chromatin interaction analysis has become important for understanding 3D topological structure of a genome as well as for linking distal cis‐regulatory elements to their target genes. Compared to the Hi‐C method, chromatin interaction analysis by paired‐end tag sequencing (ChIA‐PET) is unique, in that one can interrogate thousands of chromatin interactions (in a genome) mediated by a specific protein of interest at high resolution and reasonable cost. However, because of the noisy nature of the data, efficient analytical tools have become necessary. Here, we review some new computational methods recently developed by us and compare them with other existing methods. Our intention is to help readers to better understand ChIA‐PET results and to guide the users on selection of the most appropriate tools for their own projects.