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

Methods. 2015 Jan 15:72:65-75. doi: 10.1016/j.ymeth.2014.10.031. Epub 2014 Nov 6.


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.

Keywords: Bioinformatics; Chromatin structure; Chromosome conformation capture; Deep sequencing; Hi-C.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Chromatin / chemistry
  • Chromatin / metabolism*
  • Chromosome Mapping / methods
  • Data Interpretation, Statistical
  • Datasets as Topic
  • Genome, Human
  • Genomics / methods*
  • High-Throughput Nucleotide Sequencing
  • Humans
  • Molecular Conformation
  • Nucleic Acid Conformation*


  • Chromatin