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Bioinformatics Advance Access originally published online on February 4, 2009
Bioinformatics 2009 25(7):954-955; 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 1–4,{dagger}, Pierre Cauchy 4,5,{dagger}, Romain Fenouil 1–4,{dagger}, Adrien Jeanniard 1–4, Frederic Koch 1–4, Sébastien Jaeger 1–4, Denis Thieffry 4,5, Jean Imbert 4,5, Jean-Christophe Andrau 1–4,*, Salvatore Spicuglia 1–4,* and Pierre Ferrier 1–4,*

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

*To whom correspondence should be addressed.


  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 ChIP-on-chip Analysis Suite (CoCAS), a standalone software suite which implements optimized ChIP-on-chip data normalization, 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 datasets, 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

Supplementary information: Supplementary data are available at Bioinformatics online.

{dagger}The authors wish it to be known that, in their opinion, the first three authors should be regarded as joint First Authors.

Associate Editor: Martin Bishop

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

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