Juicer provides a one-click system for analyzing loop-resolution Hi-C experiments

By Neva C. Durand, Muhammad Saad Shamim, Ido Machol, Suhas S. P. Rao, Miriam H. Huntley, Eric S. Lander, Erez Lieberman Aiden. Cell Systems, 2016

3,341 citations recorded by the source corpus.

Hi-C experiments explore the three-dimensional 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/

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/69035c339f9397ee3749dc0906857572165890a9

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Citations in the corpus

Cohesin loss eliminates all loop domains (2017, methodology): “We first annotated loops in our maps for auxin-treated RAD21-mAC cells using default HiCCUPS parameters for 5,10, and 25kb resolutions (Durand et al., 2016b; Rao et al., 2014) with the additional requirement that the peak pixel show less than 4.5-fold enrichment over local expecteds (in order to…”
The UCSC Genome Browser database: 2021 update (2020, background): “Hi-C data from custom tracks and track hubs can also be visualized (40,44,45).”
Topologically associating domains and chromatin loops depend on cohesin and are regulated by CTCF, WAPL, and PDS5 proteins (2017, neutral): “7.5 (Durand et al, 2016).”
Towards complete and error-free genome assemblies of all vertebrate species (2020, background): “-a INT minimum number of barcodes for each molecule [5]”
Juicebox.js Provides a Cloud-Based Visualization System for Hi-C Data (2017, positive): “Juicebox.js is designed to work with data in the hic format (Durand et al., 2016a), a compressed indexed format that enables fast queries and can be used with a wide variety of contact mapping experiments, such as dilution Hi-C (Lieberman-Aiden et al., 2009), in situ Hi-C (Rao et al., 2014),…”
De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds (2016, methodology): “txt) as generated by the Juicer pipeline (22).”
Galaxy HiCExplorer 3: a web server for reproducible Hi-C, capture Hi-C and single-cell Hi-C data analysis, quality control and visualization (2020, methodology): “This tool supports loading matrices of cool, HiCExplorers h5, Juicers hic, Homer and HiCPro format and can convert them to cool, h5, Homer and ginteractions (30) format. hicNormalize.”
Juicebox Provides a Visualization System for Hi-C Contact Maps with Unlimited Zoom (2016, neutral): “…own experimental data d Users can zoom in and out of a contact map in real time d Maps can be compared to 1D tracks, 2D feature sets, or one another Durand et al., 2016, Cell Systems 3, 99–101 July 27, 2016 ª 2016 Elsevier Inc. http://dx.doi.org/10.1016/j.cels.2015.07.012 Authors Neva C. Durand,…”