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

doi:10.1016/j.cels.2016.07.002

. 2016 Jul;3(1):95-8.

doi: 10.1016/j.cels.2016.07.002.

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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References

1. Grant CE, Bailey TL, Noble WS. FIMO: Scanning for occurrences of a given motif. Bioinformatics. 2011;27(7):1017–1018. - PMC - PubMed
1. Knight PA, Ruiz D. A fast algorithm for matrix balancing. IMA J Numer Anal. 2012;33:1029–1047.
1. Lieberman-Aiden E, van Berkum N, Williams L, Imakaev M, Ragoczy T, Telling A, Amit I, Lajoie B, Sabo P, Dorschner M, et al. Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science. 2009;326:289–293. - PMC - PubMed
1. Rao SSP, Huntley MH, Durand NC, Stamenova EK, Bochkov ID, Robinson JT, Sanborn AL, Machol I, Omer AD, Lander ES, Aiden EL. A Three-dimensional Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping. Cell. 2014;159:1665–1680. - PMC - PubMed
1. Sanborn AL, Rao SSP, Huang S, Durand NC, Huntley MH, Jewett AI, Bochkov ID, Chinnappan D, Cutkosky A, Geeting KP, Gnirke A, Melnikov A, McKenna D, Stamenova EK, Lander ES, Aiden EL. Chromatin extrusion explains key features of loop and domain formation in wild-type and engineered genomes. Proceedings of the National Academy of Sciences. 2015;112(47):E6456–E6465. - PMC - PubMed

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[1] Grant CE, Bailey TL, Noble WS. FIMO: Scanning for occurrences of a given motif. Bioinformatics. 2011;27(7):1017–1018. - PMC - PubMed

[2] Grant CE, Bailey TL, Noble WS. FIMO: Scanning for occurrences of a given motif. Bioinformatics. 2011;27(7):1017–1018. - PMC - PubMed

[3] Knight PA, Ruiz D. A fast algorithm for matrix balancing. IMA J Numer Anal. 2012;33:1029–1047.

[4] Knight PA, Ruiz D. A fast algorithm for matrix balancing. IMA J Numer Anal. 2012;33:1029–1047.

[5] Lieberman-Aiden E, van Berkum N, Williams L, Imakaev M, Ragoczy T, Telling A, Amit I, Lajoie B, Sabo P, Dorschner M, et al. Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science. 2009;326:289–293. - PMC - PubMed

[6] Lieberman-Aiden E, van Berkum N, Williams L, Imakaev M, Ragoczy T, Telling A, Amit I, Lajoie B, Sabo P, Dorschner M, et al. Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science. 2009;326:289–293. - PMC - PubMed

[7] Rao SSP, Huntley MH, Durand NC, Stamenova EK, Bochkov ID, Robinson JT, Sanborn AL, Machol I, Omer AD, Lander ES, Aiden EL. A Three-dimensional Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping. Cell. 2014;159:1665–1680. - PMC - PubMed

[8] Rao SSP, Huntley MH, Durand NC, Stamenova EK, Bochkov ID, Robinson JT, Sanborn AL, Machol I, Omer AD, Lander ES, Aiden EL. A Three-dimensional Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping. Cell. 2014;159:1665–1680. - PMC - PubMed

[9] Sanborn AL, Rao SSP, Huang S, Durand NC, Huntley MH, Jewett AI, Bochkov ID, Chinnappan D, Cutkosky A, Geeting KP, Gnirke A, Melnikov A, McKenna D, Stamenova EK, Lander ES, Aiden EL. Chromatin extrusion explains key features of loop and domain formation in wild-type and engineered genomes. Proceedings of the National Academy of Sciences. 2015;112(47):E6456–E6465. - PMC - PubMed

[10] Sanborn AL, Rao SSP, Huang S, Durand NC, Huntley MH, Jewett AI, Bochkov ID, Chinnappan D, Cutkosky A, Geeting KP, Gnirke A, Melnikov A, McKenna D, Stamenova EK, Lander ES, Aiden EL. Chromatin extrusion explains key features of loop and domain formation in wild-type and engineered genomes. Proceedings of the National Academy of Sciences. 2015;112(47):E6456–E6465. - PMC - PubMed

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

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

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