Why do I have high read duplication rates in my CUT&Tag data?

High read duplicate rates are common in CUT&Tag due to assay sensitivity and extremely low background.

In general, duplication rates are higher for low abundant PTMs (H3K4me3; 50-70%) compared abundant PTMs (H3K27me3 positive control; 10-30%). High read duplicate rates are also common when profiling from low inputs, where additional PCR cycles and deeper sequencing are need to capture read diversity.

Based on EpiCypher's CUT&Tag optimization studies and analyses of published datasets, duplication rates below 70% do not impact sequencing data quality. Duplicates can be assessed and removed using Picard (broadinstitute.github.io/picard).

However, if duplications rates are a concern, there are troubleshooting options, as outlined in this article.