Is there a bias with ChIP-Seq data because promoters tend to be GC-rich and tend to be open chromatin regions?
There is definitely a connection between GC content and open chromatin regions such as promoters, CpG islands etc., but it may not be the only reason why there is a GC bias in ChIP-seq data. For example, ChIP-seq data is still susceptible to general platform specific GC biases. – answered by Tovah Markowitz, Paul Schaughency, Vishal Koparde.
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