---
title: "CUT&RUN Troubleshooting Guide | Common Issues & Solutions"
slug: "troubleshooting-cut-and-run"
description: "Troubleshoot common CUT&RUN issues, including low yield, high background, poor enrichment, library quality, and sequencing results."
updated: 2025-10-28T17:11:48Z
published: 2025-10-28T17:11:48Z
canonical: "support.epicypher.com/troubleshooting-cut-and-run"
---

> ## Documentation Index
> Fetch the complete documentation index at: https://support.epicypher.com/llms.txt
> Use this file to discover all available pages before exploring further.

# Troubleshooting guidelines for CUT&RUN

Below we outline the main areas of concern and general considerations for troubleshooting CUTANA™ CUT&RUN assays. For ALL troubleshooting, we recommend reviewing the basic quality control metrics in **Figure 1**.

- What is your cell/sample type? See [Sample Prep section](https://support.epicypher.com/docs/sample-prep-cut-and-run) for specific recommendations.
- Are Digitonin permeabilization conditions optimized for your cell type?
- Have you confirmed ConA bead binding?
- Are ConA beads brown and stored at 4˚C? ConA beads should NEVER be frozen.
- Are you using the recommended 500,000 cells per reaction? Success from low cell numbers depends on antibody quality and target abundance. Review [this article](/v1/docs/optimize-cut-and-run-targets-cells) for guidance.
- Have you included reactions with control antibodies and the K-MetStat Panel? These controls are crucial for troubleshooting CUT&RUN, as outlined [here](/v1/docs/using-snap-cutana-spike-ins-to-troubleshoot-workflows).
- Have reactions been mixed properly using a nutator? End-over-end rotation can result in ConA beads becoming clumpy or dried out during the protocol, which is why traditional rotators should be avoided.
- Did you notice significant clumping throughout the CUT&RUN protocol? If so, we recommend using the CUTANA™ Wash Buffer Enhancer Set (EpiCypher [14-1803](https://www.epicypher.com/product/cutana-wash-buffer-enhancer-set/)) in your starting buffers.
- If your continue to observe very low yields (< 5 ng) despite following the above guidelines, see [this article](/v1/docs/what-should-i-do-if-i-have-low-cut-and-run-yields).

![](https://cdn.document360.io/1fc69f91-cf1e-45ab-bc51-4063eb80e37c/Images/Documentation/image(4).png)

**Figure 1.** Overview of CUTANA CUT&RUN quality control metrics.