PT  - JOURNAL ARTICLE
AU  - Riccardo Calandrelli
AU  - Qiuyang Wu
AU  - Jihong Guan
AU  - Sheng Zhong
TI  - GITAR: an Open Source Tool for Analysis and Visualization of Hi-C Data
AID  - 10.1101/259515
DP  - 2018 Jan 01
TA  - bioRxiv
PG  - 259515
4099  - http://biorxiv.org/content/early/2018/05/08/259515.short
4100  - http://biorxiv.org/content/early/2018/05/08/259515.full
AB  - 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 GITAR (Genome Interaction Tools and Resources), a software to perform a comprehensive Hi-C data analysis, including data preprocessing, normalization, visualization and topologically associated domains (TADs) analysis. GITAR is composed of two main modules: 1) HiCtool, a Python library to process and visualize Hi-C data, including TADs 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 topological domain coordinates. A large collection of standardized processed data allows to compare different datasets in a consistent way and it saves time of work to obtain data for visualization or additional analyses. GITAR enables users without any programming or bioinformatic expertise to work with Hi-C data and it is freely available for the public at http://genomegitar.org as an open source software.