Empowering the detection of ChIP-seq "basic peaks" (bPeaks) in small eukaryotic genomes with a web user-interactive interface.
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.
['Denecker|Thomas|T|http://orcid.org/0000-0003-1421-7641', 'Lelandais|Gaëlle|G|']
D001665:Binding Sites D047369:Chromatin Immunoprecipitation D019295:Computational Biology D056890:Eukaryota D016678:Genome D059014:High-Throughput Nucleotide Sequencing D020407:Internet D011485:Protein Binding D014584:User-Computer Interface
ChIP-seq bPeaks Small eukaryotic genomes Peak calling Protein DNA-binding sites