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

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.

PMID: 27467249
PMCID: PMC5846465
DOI: 10.1016/j.cels.2016.07.002

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

Neva C Durand et al. Cell Syst. 2016 Jul.

. 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.

PMID: 27467249
PMCID: PMC5846465
DOI: 10.1016/j.cels.2016.07.002

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/.

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Figures

**Figure 1. Juicer analyzes terabases of Hi-C data with one click**
(A) Sequenced read pairs (horizontal bars) are aligned to the genome in parallel. Color indicates genomic position. Read pairs aligning to more than two positions are excluded. Those remaining are sorted by position and merged into a single list, at which point duplicate reads are removed. The *.hic* file stores contact matrices at many resolutions, which can be loaded into Juicebox for visualization. See Table S2. (B) Contact domains (yellow) are annotated using the Arrowhead algorithm. (C) Loops (cyan) are annotated using HiCCUPS.

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Comment in

Minute-Made Data Analysis: Tools for Rapid Interrogation of Hi-C Contacts.
Rowley MJ, Corces VG. Rowley MJ, et al. Mol Cell. 2016 Oct 6;64(1):9-11. doi: 10.1016/j.molcel.2016.09.029. Mol Cell. 2016. PMID: 27716489 Free PMC article.

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

Affiliations

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

Authors

Affiliations

Abstract

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References

Publication types

MeSH terms

Grants and funding

LinkOut - more resources

Full Text Sources

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