Empowering the detection of ChIP-seq “basic peaks” (bPeaks) in small eukaryotic genomes with a web user-interactive interface

BMC Research Notes. 2018;11(1):1-7 DOI 10.1186/s13104-018-3802-y

 

Journal Homepage

Journal Title: BMC Research Notes

ISSN: 1756-0500 (Online)

Publisher: BMC

LCC Subject Category: Medicine | Science: Biology (General)

Country of publisher: United Kingdom

Language of fulltext: English

Full-text formats available: PDF, HTML

 

AUTHORS

Thomas Denecker (Institut de Biologie Intégrative de la Cellule (I2BC), Centre National de la Recherche Scientifique: UMR9198, Université Paris-Saclay, Université Paris-Sud - Paris 11)
Gaëlle Lelandais (Institut de Biologie Intégrative de la Cellule (I2BC), Centre National de la Recherche Scientifique: UMR9198, Université Paris-Saclay, Université Paris-Sud - Paris 11)

EDITORIAL INFORMATION

Blind peer review

Editorial Board

Instructions for authors

Time From Submission to Publication: 15 weeks

 

Abstract | Full Text

Abstract Objective bPeaks is a peak calling program to detect protein DNA-binding sites from ChIPseq data in small eukaryotic genomes. The simplicity of the bPeaks method is well appreciated by users, but its use via an R package is challenging and time-consuming for people without programming skills. In addition, user feedback has highlighted the lack of a convenient way to carefully explore bPeaks result files. In this context, the development of a web user interface represents an important added value for expanding the bPeaks user community. Results We developed a new bPeaks application (bPeaks App). The application allows the user to perform all the peak-calling analysis steps with bPeaks in a few mouse clicks via a web browser. We added new features relative to the original R package, particularly the possibility to import personal annotation files to compare the location of the detected peaks with specific genomic elements of interest of the user, in any organism, and a new organization of the result files which are directly manageable via a user-interactive genome browser. This significantly improves the ability of the user to explore all detected basic peaks in detail.