Minute-Made Data Analysis: Tools for Rapid Interrogation of Hi-C Contacts

Abstract

Juicer and Juicebox, described by Durand et al. (2016a, 2016b), are two new tools for fast and reliable processing of Hi-C data, providing approaches for read processing, multiple normalization schemes, feature annotation, and dynamic browsing of chromatin contacts, thus reducing arduous Hi-C analysis into an easy yet flexible pipeline.

Figure 1. Functionality of Juicer and Juicebox

(A) Juicer streamlines Hi-C processing while maintaining flexibility. All standard Hi-C processing steps are performed by Juicer, as are the creation of contact maps using several different normalization methods and at many different resolutions. Processed Hi-C contact maps are stored in a compact binary format, which can be used in conjunction with Juicebox as well as with incorporated tools for feature identification. (B) Juicebox allows dynamic browsing of Hi-C data. Through Juicebox, Hi-C contacts are viewed as browsable maps, providing users with control over the resolution, normalization method, zoom, and intensity scale. Juicebox also supports the overlay of 2D and 1D annotation tracks. Hi-C data from GM12878 cells processed by Juicer and Juicebox is shown for one region at different resolutions, normalizations, zoom, and intensity scales.