Impact of genome assembly status on ChIP-Seq and ChIP-PET data mapping.
Ontology highlight
ABSTRACT: Background
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 (e.g. human and mouse).Findings
Here, we used in silico simulations to assess the impact of completeness or fragmentation of genome assemblies on ChIP-Seq and ChIP-PET data mapping.Conclusions
Most currently published genome assemblies are suitable for mapping the short sequence tags produced by ChIP-Seq or ChIP-PET.
SUBMITTER: Buisine N
PROVIDER: S-EPMC2804576 | biostudies-literature | 2009 Dec
REPOSITORIES: biostudies-literature
Publications
Impact of genome assembly status on ChIP-Seq and ChIP-PET data mapping.
Buisine Nicolas N Sachs Laurent L
BMC research notes 20091216
<h4>Background</h4>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 (e.g. human and mouse).<h4>Findings</h4>Here, we used in silico simulations to assess the impact of completeness or fr ...[more]
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