Nebula – a web-server for advanced ChIP-seq data analysis.

Nebula is 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.

(1) peak calling with FindPeaks and a module for immunoprecipitation quality control,

(2) de novo motif discovery with ChIPMunk,

(3) calculation of the density and the cumulative distribution of peak locations relative to gene transcription start sites,

(4) annotation of peaks with genomic features, and

(5) annotation of genes with peak information.

Nebula generates the graphs and the enrichment statistics at each step of the process. During steps 3 to 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.

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