Juicer Provides a One-Click System for Analyzing Loop-Resolution Hi-C Experiments

Neva C Durand; Muhammad S Shamim; Ido Machol; Suhas S P Rao; Miriam H Huntley; Eric S Lander; Erez Lieberman Aiden

doi:10.1016/j.cels.2016.07.002

Juicer Provides a One-Click System for Analyzing Loop-Resolution Hi-C Experiments

Cell Syst. 2016 Jul;3(1):95-8. doi: 10.1016/j.cels.2016.07.002.

Authors

Neva C Durand¹, Muhammad S Shamim², Ido Machol², Suhas S P Rao³, Miriam H Huntley⁴, Eric S Lander⁵, Erez Lieberman Aiden⁶

Affiliations

¹ The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Computer Science and Department of Computational and Applied Mathematics, Rice University, Houston, TX 77005, USA; Broad Institute of Harvard and Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA.
² The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Computer Science and Department of Computational and Applied Mathematics, Rice University, Houston, TX 77005, USA.
³ The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Computer Science and Department of Computational and Applied Mathematics, Rice University, Houston, TX 77005, USA; School of Medicine, Stanford University, Stanford, CA 94305, USA.
⁴ The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Computer Science and Department of Computational and Applied Mathematics, Rice University, Houston, TX 77005, USA; John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138, USA.
⁵ Broad Institute of Harvard and Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA; Department of Biology, MIT, Cambridge, MA 02139, USA; Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA.
⁶ The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Computer Science and Department of Computational and Applied Mathematics, Rice University, Houston, TX 77005, USA; Broad Institute of Harvard and Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA; Center for Theoretical Biological Physics, Rice University, Houston, TX 77030, USA. Electronic address: erez@erez.com.

Abstract

Hi-C experiments explore the 3D structure of the genome, generating terabases of data to create high-resolution contact maps. Here, we introduce Juicer, an open-source tool for analyzing terabase-scale Hi-C datasets. Juicer allows users without a computational background to transform raw sequence data into normalized contact maps with one click. Juicer produces a hic file containing compressed contact matrices at many resolutions, facilitating visualization and analysis at multiple scales. Structural features, such as loops and domains, are automatically annotated. Juicer is available as open source software at http://aidenlab.org/juicer/.

Juicer Provides a One-Click System for Analyzing Loop-Resolution Hi-C Experiments

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