ChIAPoP: a new tool for ChIA-PET data analysis

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...

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Detalles Bibliográficos
Autores principales: Huang, Weichun, Medvedovic, Mario, Zhang, Jingwen, Niu, Liang
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2019
Materias:
Methods Online
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6468250/
https://www.ncbi.nlm.nih.gov/pubmed/30753588
http://dx.doi.org/10.1093/nar/gkz062
Descripción
Sumario: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.

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