How did you determine that a NG-seq sequencing depth of 3 to 5 million sequencing reads was sufficient for CUT&RUN analysis?

This decision was based on our analysis of hundreds of CUT&RUN samples. We found that a sequencing depth lower than 3 million generated too few peaks and that the number of peaks increased with deeper sequencing. If desired, one can increase the sequencing depth to 10 million reads per sample. The duplication rate of sequencing reads significantly increases if the sequencing depth is >15 million reads per sample. Typically, the more effective the antibody is in the assay, the less sequencing depth is needed to obtain a good result.

Last updated: February 24, 2026