Can you use ChIP-seq data to analyze copy number variants? Can you do structural variant calling?
Possibly. Theoretically you can see both CNV changes and structural variants in the ChIP-seq data and the Input controls, but the coverage will be much lower than needed to confidently call either. Although not robust, input samples can be used to look for relative trends in copy number over large windows. For ChIP-seq data, copy number variants is also often confounded by changes in protein binding pattern as well. It is much better to use whole genome sequencing or whole exome sequencing to answer these questions. – answered by Tovah Markowitz, Paul Schaughency, Vishal Koparde.
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