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an integrated chip-seq analysis platform with customizable workflows一个集成chip-seq和可定制的工作流分析平台
Giannopoulou and Elemento BMC Bioinformatics 2011, 12:277
/1471-2105/12/277
SOFTWARE Open Access
An integrated ChIP-seq analysis platform with
customizable workflows
Eugenia G Giannopoulou1,2 and Olivier Elemento1,2*
Abstract
Background: Chromatin immunoprecipitation followed by next generation sequencing (ChIP-seq), enables
unbiased and genome-wide mapping of protein-DNA interactions and epigenetic marks. The first step in ChIP-seq
data analysis involves the identification of peaks (i.e., genomic locations with high density of mapped sequence
reads). The next step consists of interpreting the biological meaning of the peaks through their association with
known genes, pathways, regulatory elements, and integration with other experiments. Although several programs
have been published for the analysis of ChIP-seq data, they often focus on the peak detection step and are usually
not well suited for thorough, integrative analysis of the detected peaks.
Results: To address the peak interpretation challenge, we have developed ChIPseeqer, an integrative,
comprehensive, fast and user-friendly computational framework for in-depth analysis of ChIP-seq datasets. The
novelty of our approach is the capability to combine several computational tools in order to create easily
customized workflows that can be adapted to the user’s needs and objectives. In this paper, we describe the main
components of the ChIPseeqer framework, and also demonstrate the utility and diversity of the analyses offered,
by analyzing a published ChIP-seq dataset.
Conclusions: ChIPseeqer facilitates ChIP-seq data analysis by offering a flexible and powerful set of computational
tools that can be used in combination with one another. The framework is freely available as a user-friendly GUI
application, but all programs are also executable from
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