Should I perform single-end sequencing or pair-end sequencing for CUT&RUN?

Although publications usually recommend pair-end sequencing for CUT&RUN assay, we find that single-end sequencing works as well. Which one to choose depends on if you would like to know the size of the CUT&RUN DNA fragments, as this information is only provided by pair-end sequencing. If you are only interested in the genomic binding loci of the target protein, but not the length of each DNA fragment by MNase digestion, then single-end sequencing is fine and cost-effective. 

Last updated: February 26, 2024