---
title: "How do I confirm the quality of my CUT&RUN sequencing library?"
slug: "confirm-quality-of-sequencing-library"
updated: 2024-10-01T17:17:43Z
published: 2024-10-01T17:17:43Z
canonical: "support.epicypher.com/confirm-quality-of-sequencing-library"
---

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# How do I confirm the quality of my CUT&RUN sequencing library?

There are two general approaches to confirming the quality of your CUT&RUN sequencing library, outlined below.

## **Library yields**

- In general, library yields should not be used to determine assay success. Library yields vary widely by cell type, number of cells, target abundance, and antibody quality.
- Aim for a library concentration of ≥ 1 nM, which will enable pooling at standard concentrations for multiplexed sequencing.
- For library concentrations below 0.5 nM, see [see this article](/v1/docs/cut-and-run-sequence-low-concentration).

## **Fragment distribution of purified library**

- Fragment distribution analysis of purified sequencing libraries is the single BEST method to confirm CUT&RUN success.
- Libraries should show enrichment of mononucleosome-sized DNA fragments at ~300 bp, which includes CUT&RUN DNA + sequencing adapters (see **Figure** **1**).

![tapestation trace resized@2x-8](https://cdn.document360.io/1fc69f91-cf1e-45ab-bc51-4063eb80e37c/Images/Documentation/tapestation%20trace%20resized@2x-8.png)

**Figure 1.** Typical TapeStation traces from CUTANA™ CUT&RUN libraries prepared using antibodies targeting IgG (EpiCypher 13-0042), H3K4me3 (EpiCypher 13-0060), and CTCF (EpiCypher 13-2014). All libraries are predominantly enriched for mononucleosome-sized fragments, as indicated by the peak at ~300 bp (~170 bp nucleosomes + sequencing adapters).