GITAR: An Open Source Tool for Analysis and Visualization of Hi-C Data.
10.1016/j.gpb.2018.06.006
- Author:
Riccardo CALANDRELLI
1
;
Qiuyang WU
2
;
Jihong GUAN
2
;
Sheng ZHONG
3
Author Information
1. Department of Bioengineering, University of California San Diego, La Jolla, CA 92093, USA. Electronic address: rcalandrelli@eng.ucsd.edu.
2. Department of Computer Science and Technology, Tongji University, Shanghai 200092, China.
3. Department of Bioengineering, University of California San Diego, La Jolla, CA 92093, USA.
- Publication Type:Journal Article
- Keywords:
Chromatin interaction;
Hi-C data normalization;
Pipeline;
Processed Hi-C data library;
Topologically-associated domain
- MeSH:
Animals;
Chromatin;
chemistry;
Computer Graphics;
Genome;
Genomics;
methods;
Humans;
Mice;
Software
- From:
Genomics, Proteomics & Bioinformatics
2018;16(5):365-372
- CountryChina
- Language:English
-
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.
