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

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, use...

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Bibliographic Details
Published in:BMC research notes 2018-10, Vol.11 (1), p.698-698, Article 698
Main Authors: Denecker, Thomas, Lelandais, Gaëlle
Format: Article
Language:English
Subjects:
Analysis
Binding Sites
Bioinformatics
bPeaks
ChIP-seq
Chromatin Immunoprecipitation
Computational Biology - methods
Data processing
Deoxyribonucleic acid
DNA
Empowerment
Eukaryota - genetics
Eukaryotes
Gene expression
Genome - genetics
Genomes
Genomics
High-Throughput Nucleotide Sequencing
Internet
Life Sciences
Peak calling
Peak load
Protein Binding
Protein DNA-binding sites
Proteins
Research Note
Small eukaryotic genomes
Software
Transcription factors
User-Computer Interface
Web browsers
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Description
Summary: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. 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.
ISSN:1756-0500
1756-0500
DOI:10.1186/s13104-018-3802-y