---
title: "Why Is There Background in Open Chromatin in CUT&RUN Data?"
slug: "why-is-there-background-in-open-chromatin-in-my-sequencing-data"
description: "Learn why open chromatin background occurs in CUT&RUN sequencing data and how to reduce it by optimizing digestion and sequencing depth."
updated: 2024-09-05T18:26:05Z
published: 2024-09-05T18:26:05Z
canonical: "support.epicypher.com/why-is-there-background-in-open-chromatin-in-my-sequencing-data"
---

> ## 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.

# Why is there background in open chromatin in my sequencing data?

Background in open chromatin may indicate digestion of accessible chromatin by pAG-MNase, due to prolonged incubation and/or incorrect temperature. However, it can also indicate over-sequencing of CUT&RUN libraries.

To resolve this:

- Sequence libraries to 3-8 million reads.
- Repeat assay using fresh buffers.
- Ensure pAG-MNase digestion is performed at 4˚C.