National Exposure Research Laboratory, Environmental Protection Agency, Research Triangle Park, NC 27709, USA.
Division of Biostatistics and Bioinformatics, Department of Environmental Health, College of Medicine, University of Cincinnati, Cincinnati, OH 45267, USA.
Nucleic Acids Res. 2019 Apr 23;47(7):e37. doi: 10.1093/nar/gkz062.
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.
染色质互作分析通过末端配对标签测序（ChIA-PET）是一种研究蛋白质介导的全基因组染色质互作的流行方法。ChIA-PET 数据分析的主要目标是检测 DNA 区域之间的相互作用。在这里，我们提出了一种新的方法和相关的数据分析流程 ChIAPoP，用于从 ChIA-PET 数据中检测染色质相互作用。我们将 ChIAPoP 与其他流行的方法进行了比较，包括超几何模型（用于 ChIA-PET 工具）、MICC（用于 ChIA-PET2）、ChiaSig 和 mango。结果表明，ChIA-PoP 在检测真实染色质相互作用方面的性能优于或至少与这些顶级现有方法相当。ChIAPoP 可在 https://github.com/wh90999/ChIAPoP 上免费获得。
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