Abstract
Interactions between chromatin segments play a large role in functional genomic assays and developments in genomic interaction detection methods have shown interacting topological domains within the genome. Among these methods, Hi-C plays a key role. Here, we present the Genome Interaction Tools and Resources (GITAR), a software to perform a comprehensive Hi-C data analysis, including data preprocessing, normalization, and visualization, as well as analysis of topologically-associated domains (TADs). GITAR is composed of two main modules: (1) HiCtool, a Python library to process and visualize Hi-C data, including TAD analysis; and (2) processed data library, a large collection of human and mouse datasets processed using HiCtool. HiCtool leads the user step-by-step through a pipeline, which goes from the raw Hi-C data to the computation, visualization, and optimized storage of intra-chromosomal contact matrices and TAD coordinates. A large collection of standardized processed data allows the users to compare different datasets in a consistent way, while saving time to obtain data for visualization or additional analyses. More importantly, GITAR enables users without any programming or bioinformatic expertise to work with Hi-C data. GITAR is publicly available at http://genomegitar.org as an open-source software.
Highlights
Genomes are more than linear sequences, with DNA folding-up into elaborate physical structures that allow for extreme spatial compactness of the genetic material and play an important role in epigenetic regulation [1, 2]
During the past fifteen years, several techniques have been developed to explore the architecture of genomes, such as Chromosome Conformation Capture (3C) [3], Circular Chromosome Conformation Capture (4C) [4], Chromosome Conformation Capture Carbon Copy (5C) [5], Hi-C [6] and ChIA-PET [7]
We developed HiCtool, a pipeline to process and visualize Hi-C data, including topologically associated domains (TADs) analysis
Summary
Genomes are more than linear sequences, with DNA folding-up into elaborate physical structures that allow for extreme spatial compactness of the genetic material and play an important role in epigenetic regulation [1, 2]. We developed HiCtool, a pipeline to process and visualize Hi-C data, including topologically associated domains (TADs) analysis. Visualizing the data in heatmaps (normalized and “observed over expected” contact)
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
