CoCAS: a ChIP-on-chip analysis suite

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.

Supplementary information: Supplementary data are available at Bioinformatics online.

Fig. 1.

Stepwise data analysis of Suz12 ChIP-on-chip in CoCAS. Quality control reports include (A) density plots of immunoprecipitated (IP) DNA, in red, and Input DNA, in green, so as to detect any dye bias; (B) MA plots which allow assessment of normalization quality and probe enrichment; (C) replicate correlation plots, which also help estimate background noise (which shows no correlation at low intensities). (D) Chromosomal view (chromosome 6) of Suz12 IP over input log ratios (in red) via IGB (top), followed by peak detection (green track) on a close up in the Hox cluster region (bottom).