Impact of genome assembly status on ChIP-Seq and ChIP-PET data mapping
Nicolas Buisine1, Laurent Sachs
1Department Evolution des Régulation Endocriniennes, Museum National d'Histoire Naturelle, 7, Rue Cuvier, 75231 Paris Cedex 05, France.
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.
More Related Videos
11:13RNA-Seq Analysis of Differential Gene Expression in Electroporated Chick Embryonic Spinal Cord
Published on: November 1, 2014
09:06High-throughput Identification of Gene Regulatory Sequences Using Next-generation Sequencing of Circular Chromosome Conformation Capture (4C-seq)
Published on: October 5, 2018
Related Concept Videos
Genome Annotation and Assembly
RNA-seq
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while microarray-based...
Evolutionary Relationships through Genome Comparisons
