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ChIAPoP: a new tool for ChIA-PET data analysis
Citation:
Huang, W., M. Medvedovic, J. Zhang, AND L. Niu. ChIAPoP: a new tool for ChIA-PET data analysis. NUCLEIC ACIDS RESEARCH. Oxford University Press, Cary, NC, 47(7):e37, (2019). https://doi.org/10.1093/nar/gkz062
Impact/Purpose:
Chromatin Interaction Analysis by Paired-End Tag sequencing (ChIA-PET) is emerging as an important experimental method for detecting specific protein-mediated chromatin loops genome-wide at high resolution. It is a computationally challenging task to identify true interactions from large ChIA-PET data. To address the challenging problem, we developed a new robust statistical method and an easy-to-use tool to facilitate research in this field. Our method and tool will be useful for researchers in studying chromatin interactions, gene regulation mechanism, and chromatin structure changes related to genetic and environmental changes.
Description:
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.
URLs/Downloads:
DOI: ChIAPoP: a new tool for ChIA-PET data analysis
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6468250/