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ChIAPoP: a new tool for ChIA-PET data analysis.

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.

SUBMITTER: Huang W

PROVIDER: S-EPMC6468250 | biostudies-literature | 2019 Apr

REPOSITORIES: biostudies-literature

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ChIAPoP: a new tool for ChIA-PET data analysis.

Huang Weichun W Medvedovic Mario M Zhang Jingwen J Niu Liang L

Nucleic acids research 20190401 7

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 ...[more]

PMID: 30753588

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