ChIP-seq versus other sequencing methods: What is CUT & RUN? How do you compare ChIP-seq and CUT & RUN?

CUT & RUN is a relatively new method that uses a protein A conjugated to MNase to cleave the DNA directly. The protein A, in turn, can bind to antibodies. This is reported to require less sequencing, have less background, and have an increased resolution compared to ChIP-seq. As this is a newer method, there is still an evaluation period as more labs try this method out. Many companies have begun selling the purified pA-MNase to facilitate the testing of this method. It is too early to tell if the method is a direct improvement on all aspects of ChIP-seq. – answered by Tovah Markowitz, Paul Schaughency, Vishal Koparde.