Conclusion
In summary, ChIP-seq offers an alternative to ChIP-chip. STAT1 experimental ChIP-seq data have a high degree of similarity to results obtained by ChIP-chip for the same type of experiment, with >64% of peaks in shared genomic regions. Because the data are sequence reads, ChIP-seq offers a rapid analysis pipeline (as long as a high-quality genome sequence is available for read mapping, and the genome doesn't have repetitive content that confuses the mapping process) as well as the potential to detect mutations in binding-site sequences, which may directly support any observed changes in protein binding and gene regulation.
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