What is the depth of sequencing reads per sample required in a CUT&RUN assay?

We suggest a sequencing depth of 3-5 million reads per sample, this holds true for a starting cell range of 10,000 to 250,000. Because of the very low background signal generated in CUT&RUN, this sequencing depth is usually sufficient for histone modifications and transcription factors. We have found that less than 3 million does not work and greater than 15 million greatly increases the number of duplicate reads.

Last updated: February 24, 2026