RT Journal Article SR Electronic T1 HiCRep: assessing the reproducibility of Hi-C data using a stratum-adjusted correlation coefficient JF bioRxiv FD Cold Spring Harbor Laboratory SP 101386 DO 10.1101/101386 A1 Tao Yang A1 Feipeng Zhang A1 Galip Gurkan Yardimci A1 Ross C. Hardison A1 William Stafford Noble A1 Feng Yue A1 Qunhua Li YR 2017 UL http://biorxiv.org/content/early/2017/01/18/101386.abstract AB 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.