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Bacon: a comprehensive computational benchmarking framework for evaluating targeted chromatin conformation capture-specific methodologies.

ABSTRACT: Chromatin conformation capture (3C)-based technologies have enabled the accurate detection of topological genomic interactions, and the adoption of ChIP techniques to 3C-based protocols makes it possible to identify long-range interactions. To analyze these large and complex datasets, computational methods are undergoing rapid and expansive evolution. Thus, a thorough evaluation of these analytical pipelines is necessary to identify which commonly used algorithms and processing pipelines need to be improved. Here we present a comprehensive benchmark framework, Bacon, to evaluate the performance of several computational methods. Finally, we provide practical recommendations for users working with HiChIP and/or ChIA-PET analyses.

SUBMITTER: Tang L

PROVIDER: S-EPMC8780810 | biostudies-literature | 2022 Jan

REPOSITORIES: biostudies-literature

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Bacon: a comprehensive computational benchmarking framework for evaluating targeted chromatin conformation capture-specific methodologies.

Tang Li L Hill Matthew C MC Ellinor Patrick T PT Li Min M

Genome biology 20220121 1

Chromatin conformation capture (3C)-based technologies have enabled the accurate detection of topological genomic interactions, and the adoption of ChIP techniques to 3C-based protocols makes it possible to identify long-range interactions. To analyze these large and complex datasets, computational methods are undergoing rapid and expansive evolution. Thus, a thorough evaluation of these analytical pipelines is necessary to identify which commonly used algorithms and processing pipelines need to ...[more]

PMID: 35063001

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