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Touati Benoukraf, Pierre
Cauchy, Romain Fenouil, Adrien Jeanniard, Sébastien Jaeger, Jean
Imbert, Jean-Christophe Andrau, Salvatore Spicuglia and Pierre
Ferrier.
Abstract: High density
tiling microarrays are now widely used for the purpose of ChIP-on-chip
experiments so as to study transcription regulation. However, this
technique generates large amounts of data that are not easily usable by
non computer scientists. We present CoCAS, a standalone ChIP-on-Chip
Analysis Suite which features a novel implementation of a previously
described ChIP-on-chip optimised normalisation, as well as a
compilation of quality control reports and improved peak detection.
CoCAS can readily be used on the latest generation of Agilent
high-density arrays. Unlike other tools available, Cocas allows
dye-swap, replicate correlation and connects easily with other software
(genome browsers and peak detection). The peak detection methods
implemented in CoCAS can
be used for any set of data including ChIP-Seq data.
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