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A flexible ChIP-sequencing simulation toolkit

BACKGROUND: A major challenge in evaluating quantitative ChIP-seq analyses, such as peak calling and differential binding, is a lack of reliable ground truth data. Accurate simulation of ChIP-seq data can mitigate this challenge, but existing frameworks are either too cumbersome to apply genome-wide...

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Detalles Bibliográficos
Autores principales: Zheng, An, Lamkin, Michael, Qiu, Yutong, Ren, Kevin, Goren, Alon, Gymrek, Melissa
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8056602/
https://www.ncbi.nlm.nih.gov/pubmed/33879052
http://dx.doi.org/10.1186/s12859-021-04097-5
Descripción
Sumario:BACKGROUND: A major challenge in evaluating quantitative ChIP-seq analyses, such as peak calling and differential binding, is a lack of reliable ground truth data. Accurate simulation of ChIP-seq data can mitigate this challenge, but existing frameworks are either too cumbersome to apply genome-wide or unable to model a number of important experimental conditions in ChIP-seq. RESULTS: We present ChIPs, a toolkit for rapidly simulating ChIP-seq data using statistical models of key experimental steps. We demonstrate how ChIPs can be used for a range of applications, including benchmarking analysis tools and evaluating the impact of various experimental parameters. ChIPs is implemented as a standalone command-line program written in C++ and is available from https://github.com/gymreklab/chips. CONCLUSIONS: ChIPs is an efficient ChIP-seq simulation framework that generates realistic datasets over a flexible range of experimental conditions. It can serve as an important component in various ChIP-seq analyses where ground truth data are needed. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12859-021-04097-5.