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

• Published in: Cell systems Vol. 3; no. 1; pp. 95 - 98
• Main Authors: Durand, Neva C., Shamim, Muhammad S., Machol, Ido, Rao, Suhas S.P., Huntley, Miriam H., Lander, Eric S., Aiden, Erez Lieberman
• Format: Journal Article
• Language: English
• Published: United States Elsevier Inc 01.07.2016
• Subjects: Algorithms; Computational Biology; Genome; Software
• ISSN: 2405-4712; 2405-4720
• DOI: 10.1016/j.cels.2016.07.002

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/. [Display omitted] •Juicer enables users to process terabase scale Hi-C datasets with a single click•Juicer automatically annotates loops and contact domains•Juicer is available as open source software•Juicer is compatible with multiple cluster operating systems and with Amazon Web Services Durand et al. introduce Juicer, a one-click, end-to-end pipeline for analyzing data from Hi-C and other contact mapping experiments. Juicer generates contact matrices at multiple resolutions and identifies features including contact domains and loops.