I had great results with ChIP-qPCR, but when I did ChIP-seq only a few reactions came up with decent peaks. What could be the reason?
There is no one right answer here. You need to go through every step in the QC, deduplication, and peak calling that you have done and look for where something isn’t behaving as expected. For example, do you have too many PCR duplicates? Could you have used the wrong peak caller for your protein? – answered by Tovah Markowitz, Paul Schaughency, Vishal Koparde.
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