Measuring the reproducibility and quality of Hi-C data

In this work, we assess reproducibility and quality measures by varying sequencing depth, resolution and noise levels in Hi-C data from 13 cell lines, with two biological replicates each, as well as 176 simulated matrices. Through this extensive validation and benchmarking of Hi-C data, we describe best practices for reproducibility and quality assessment of Hi-C experiments. We make all software publicly available at http: //github. com/kundajelab/3DChromatinReplicateQC to facilitate adoption in the community.