title: The Hitchhiker's guide to Hi-C analysis: practical guidelines.
abstract: 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.
authors.affiliation: Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605-0103, USA. Electronic address: Bryan.lajoie@umassmed.edu.
authors.forename: Bryan R
authors.initials: BR
authors.lastname: Lajoie
authors.affiliation: Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605-0103, USA. Electronic address: Job.dekker@umassmed.edu.
authors.forename: Job
authors.initials: J
authors.lastname: Dekker
authors.affiliation: Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605-0103, USA. Electronic address: noam.kaplan2@gmail.com.
authors.forename: Noam
authors.initials: N
authors.lastname: Kaplan
mesh_terms: D002843:Chromatin / Q000737:chemistry / Q000378:metabolism*; D002874:Chromosome Mapping / Q000379:methods; D003627:Data Interpretation, Statistical; D066264:Datasets as Topic; D015894:Genome, Human; D023281:Genomics / Q000379:methods*; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D008968:Molecular Conformation; D009690:Nucleic Acid Conformation
chemical_list: D002843:Chromatin
keywords: Bioinformatics; Chromatin structure; Chromosome conformation capture; Deep sequencing; Hi-C