---
title: "Sequencing Low-Concentration CUT&RUN Libraries | Best Practices"
slug: "cut-and-run-sequence-low-concentration"
description: "Learn how to sequence low-concentration CUT&RUN libraries, improve library yields, and maximize sequencing success with limited DNA."
updated: 2026-02-27T15:28:28Z
published: 2026-02-27T15:28:28Z
canonical: "support.epicypher.com/cut-and-run-sequence-low-concentration"
---

> ## 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.

# Considerations when sequencing low-concentration libraries

> This article also applies to meCUT&RUN.

Low library yields are unavoidable in some experiments (e.g. mapping a low abundance target and/or using low cell numbers). For low-concentration libraries, consider the following options:

**Repeat library prep:** Use more CUT&RUN-enriched DNA input and/or increase the number of PCR cycles used for indexing PCR to improve yields for sequencing. Note that increasing the number of PCR cycles may lead to higher read duplication rates and require deeper sequencing to capture read diversity.

**Concentrate library for sequencing:** If library prep cannot be repeated, use a Speedvac to increase the library concentration and add as much of the library as possible to the sequencing pool. Deeper sequencing is recommended to ensure sufficient read depth for the the low-concentration library.

**In both cases, deeper sequencing is strongly recommended.**