Impact of genome assembly status on ChIP-Seq and ChIP-PET data mapping

• Main Authors: Sachs Laurent, Buisine Nicolas
• Format: Article
• Language: English
• Published: BMC 2009-12-01
• Series: BMC Research Notes
• Online Access: http://www.biomedcentral.com/1756-0500/2/257

<p>Abstract</p> <p>Background</p> <p>ChIP-Seq and ChIP-PET can potentially be used with any genome for genome wide profiling of protein-DNA interaction sites. Unfortunately, it is probable that most genome assemblies will never reach the quality of the human genome assembly. Therefore, it remains to be determined whether ChIP-Seq and ChIP-PET are practicable with genome sequences other than a few (<it>e.g</it>. human and mouse).</p> <p>Findings</p> <p>Here, we used <it>in silico </it>simulations to assess the impact of completeness or fragmentation of genome assemblies on ChIP-Seq and ChIP-PET data mapping.</p> <p>Conclusions</p> <p>Most currently published genome assemblies are suitable for mapping the short sequence tags produced by ChIP-Seq or ChIP-PET.</p>