Benoukraf Touati, Cauchy Pierre, Fenouil Romain, Jeanniard Adrien, Koch Frederic, Jaeger Sébastien, Thieffry Denis, Imbert Jean, Andrau Jean-Christophe, Spicuglia Salvatore, Ferrier Pierre
Centre d'Immunologie de Marseille-Luminy, CNRS, UMR6102, Inserm, U631, Université de la Méditerranée and Inserm, U928, TAGC, Marseille, France.
Bioinformatics. 2009 Apr 1;25(7):954-5. doi: 10.1093/bioinformatics/btp075. Epub 2009 Feb 4.
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.
The software is available for download along with a sample dataset at http://www.ciml.univ-mrs.fr/software/ferrier.htm.
Supplementary data are available at Bioinformatics online.
高密度平铺微阵列越来越多地与染色质免疫沉淀（ChIP）分析结合使用，以研究转录调控。为便于分析这种方法产生的大量数据，我们开发了芯片上的ChIP分析套件（CoCAS），这是一个独立的软件套件，可实现优化的芯片上的ChIP数据标准化、改进的峰检测以及质量控制报告。我们的软件允许染料交换、重复相关性分析，并能轻松连接基因组浏览器和其他峰检测算法。CoCAS可直接用于最新一代的安捷伦高密度阵列。此外，所实施的峰检测方法适用于其他数据集，包括ChIP-Seq输出。
该软件可连同示例数据集一起从http://www.ciml.univ-mrs.fr/software/ferrier.htm下载。
补充数据可在《生物信息学》在线获取。
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