ChIP-seq versus other sequencing methods: What are the advantages and disadvantages of using ChIP-seq instead of ATAC-seq?

ATAC-seq is a direct measure of open chromatin by measuring the accessibility of transposition. ChIP-seq is a more indirect method for measuring open chromatin based upon presence of certain histone marks or other protein factors. They should be thought of as complementary methods for these types of questions. If all you want to measure is open chromatin and not protein factors that associate with open chromatin, ATAC-seq is preferable. – answered by Tovah Markowitz, Paul Schaughency, Vishal Koparde.