title: Nebula--a web-server for advanced ChIP-seq data analysis.
abstract: BACKGROUND
  ChIP-seq consists of chromatin immunoprecipitation and deep sequencing of the extracted DNA fragments. It is the technique of choice for accurate characterization of the binding sites of transcription factors and other DNA-associated proteins. We present a web service, Nebula, which allows inexperienced users to perform a complete bioinformatics analysis of ChIP-seq data.
  
  
  RESULTS
  Nebula was designed for both bioinformaticians and biologists. It is based on the Galaxy open source framework. Galaxy already includes a large number of functionalities for mapping reads and peak calling. We added the following to Galaxy: (i) peak calling with FindPeaks and a module for immunoprecipitation quality control, (ii) de novo motif discovery with ChIPMunk, (iii) calculation of the density and the cumulative distribution of peak locations relative to gene transcription start sites, (iv) annotation of peaks with genomic features and (v) annotation of genes with peak information. Nebula generates the graphs and the enrichment statistics at each step of the process. During Steps 3-5, Nebula optionally repeats the analysis on a control dataset and compares these results with those from the main dataset. Nebula can also incorporate gene expression (or gene modulation) data during these steps. In summary, Nebula is an innovative web service that provides an advanced ChIP-seq analysis pipeline providing ready-to-publish results.
  
  
  BACKGROUND
  Nebula is available at http://nebula.curie.fr/
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors: Institut Curie, Paris 75248, France.
authors: Valentina
authors: V
authors: Boeva
authors: Alban
authors: A
authors: Lermine
authors: Camille
authors: C
authors: Barette
authors: Christel
authors: C
authors: Guillouf
authors: Emmanuel
authors: E
authors: Barillot
mesh_terms: D001665:Binding Sites; D047369:Chromatin Immunoprecipitation / Q000379:methods*; D019295:Computational Biology / Q000379:methods*; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D020407:Internet; D012984:Software