QuASAR: Quality Assessment of Spatial Arrangement Reproducibility in Hi-C Data

Hi-C has revolutionized global interrogation of chromosome conformation, however there are few tools to assess the reliability of individual experiments. Here we present a new approach, QuASAR, for measuring quality within and between Hi-C samples. We show that QuASAR can detect even tiny fractions of noise and estimate both return on additional sequencing and quality upper bounds. We also demonstrate QuASAR's utility in measuring replicate agreement across feature resolutions. Finally, QuASAR can estimate resolution limits based on both internal and replicate quality scores. QuASAR provides an objective means of Hi-C sample comparison while providing context and limits to these measures.