The Hitchhiker's guide to Hi-C analysis: practical guidelines.

Lajoie BR, Dekker J, Kaplan N.
Methods (San Diego, Calif.). 2015 Jan 15;72:65-75.
Over the last decade, development and application of a set of molecular genomic approaches based on the chromosome conformation capture method (3C), combined with increasingly powerful imaging approaches, have enabled high resolution and genome-wide analysis of the spatial organization of chromosomes. The aim of this paper is to provide guidelines for analyzing and interpreting data obtained with genome-wide 3C methods such as Hi-C and 3C-seq that rely on deep sequencing to detect and quantify pairwise chromatin interactions.