ChIAPoP: a new tool for ChIA-PET data analysis. Issue 7 (8th February 2019)

• Record Type: Journal Article
• Authors: Huang, Weichun; Medvedovic, Mario; Zhang, Jingwen; Niu, Liang
• Is Part Of: Nucleic acids research. Volume 47:Issue 7(2019)
• Page Start: e37
• Page End: e37
• Publication Date: 2019-02-08
• Subjects: Nucleic acids -- Periodicals; Molecular biology -- Periodicals; 572.805
• DOI: 10.1093/nar/gkz062
• Languages: English
• ISSNs: 0305-1048

Abstract

Abstract: Chromatin Interaction Analysis by Paired-End Tag Sequencing (ChIA-PET) is a popular assay method for studying genome-wide chromatin interactions mediated by a protein of interest. The main goal of ChIA-PET data analysis is to detect interactions between DNA regions. Here, we propose a new method and the associated data analysis pipeline, ChIAPoP, to detect chromatin interactions from ChIA-PET data. We compared ChIAPoP with other popular methods, including a hypergeometric model (used in ChIA-PET tool), MICC (used in ChIA-PET2), ChiaSig and mango. The results showed that ChIA-PoP performed better than or at least as well as these top existing methods in detecting true chromatin interactions. ChIAPoP is freely available to the public at https://github.com/wh90999/ChIAPoP .