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Bioinformatics Advance Access published online on February 4, 2009
Bioinformatics, doi:10.1093/bioinformatics/btp075
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©2009 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

CoCAS: A ChIP-on-chip Analysis Suite

Touati Benoukraf 1–3,5,6, Pierre Cauchy 4,6, Romain Fenouil 1–3,5,6, Adrien Jeanniard 1–3,5, Frederic Koch 1–3,5, Sébastien Jaeger 1–3,5, Denis Thieffry 4,5, Jean Imbert 4,5, Jean-Christophe Andrau 1–3,5,*, Salvatore Spicuglia 1–3,5,* and Pierre Ferrier 1–3,5,*

1Centre d'Immunologie de Marseille-Luminy, Marseille, France;
2CNRS, UMR6102, Marseille, France;
3Inserm, U631, Marseille, France;
4Inserm, U928, TAGC, Marseille, France;
5Université de la Méditerranée, Marseille, France.

*To whom correspondence should be addressed. Mr. Touati Benoukraf, E-mail: benoukraf{at}ciml.univ-mrs.fr, cauchy{at}tagc.univ-mrs.fr


  Abstract

Motivation: High-density tiling microarrays are increasingly used in combination with ChIP assays to study transcriptional regulation. To ease the analysis of the large amounts of data generated by this approach, we have developed CoCAS, a standalone software suite which implements optimised ChIP-on-chip data normalisation, improved peak detection, as well as quality control reports. Our software allows dye-swap, replicate correlation, and connects easily with genome browsers and other peak detection algorithms. CoCAS can readily be used on the latest generation of Agilent high-density arrays. Also, the implemented peak detection methods are suitable for other data sets, including ChIP-Seq output.

Availability: The software is available for download along with a sample dataset at http://www.ciml.univ-mrs.fr/software/ferrier.htm.

Contact: ferrier{at}ciml.univ-mrs.fr, andrau{at}ciml.univ-mrs.fr,spicuglia{at}ciml.univ-mrs.fr.

Associate Editor: Prof. Martin Bishop

6These authors contributed equally to this work.

Received on December 16, 2008; revised on January 30, 2009; accepted on January 30, 2009

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