TY - JOUR T1 - HiCRep: assessing the reproducibility of Hi-C data using a stratum-adjusted correlation coefficient JF - bioRxiv DO - 10.1101/101386 SP - 101386 AU - Tao Yang AU - Feipeng Zhang AU - Galip Gurkan Yardimci AU - Ross C. Hardison AU - William Stafford Noble AU - Feng Yue AU - Qunhua Li Y1 - 2017/01/01 UR - http://biorxiv.org/content/early/2017/01/18/101386.abstract N2 - Hi-C is a powerful technology for studying genome-wide chromatin interactions. However, current methods for assessing Hi-C data reproducibility ignore spatial features in Hi-C data, such as domain structure and distance dependence. We present the stratum-adjusted correlation coefficient (SCC), a reproducibility measure that accounts for these features. SCC can assess pairwise differences between Hi-C matrices under a wide range of settings and can be used to determine optimal sequencing depth. The measure consistently shows higher accuracy than existing approaches in distinguishing subtle differences in reproducibility and depicting interrelationships of cell lineages. The R package HiCRep implements our approach. ER -