---
title: "What do large DNA fragment sizes in Bioanalyzer/TapeStation mean in CUT&Tag?"
slug: "large-fragments-cut-and-tag"
tags: ["cut and tag"]
updated: 2024-11-06T21:09:01Z
published: 2024-11-06T21:09:01Z
canonical: "support.epicypher.com/large-fragments-cut-and-tag"
---

> ## 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.

# What do large DNA fragment sizes in Bioanalyzer/TapeStation mean in CUT&Tag?

Enrichment of large peaks (>700 bp) in CUT&Tag sequencing libraries can be caused by multiple factors, outlined in detail below. We recommend repeating the experiment and paying close attention to sample prep steps, bead resuspension during tagmentation and PCR, and confirming PCR cycling parameters match those in the CUTANA™ CUT&Tag [Kit Manual](https://www.epicypher.com/resources/protocols/cutana-cut-and-tag-kit-manual) and [DIY Protocol](https://www.epicypher.com/resources/protocols/cutana-pag-tn5-resources/).

- **Poor sample prep and/or poor nuclei extraction.** Poor sample prep can result in issues with ConA bead binding, bead clumping, and sample loss, affecting the entire CUT&Tag workflow. Review [quality control checks](/v1/docs/cell-sample-good-enough-cut-and-tag) for starting cells, the [nuclei extraction protocol](/v1/docs/nuclei-extraction-cut-and-tag), and reference [sample prep steps and variations](/v1/docs/sample-prep-cut-and-tag) if applicable.
- **Problems with ConA bead resuspension.** Excessive bead clumping impacts CUT&Tag data quality. It is especially critical to keep ConA beads resuspended during pAG-Tn5 binding, tagmentation, and indexing PCR. Proper bead mixing helps ensure even distribution of pAG-Tn5 across nuclei, robust Tn5 activation, and maximizes PCR efficiency.
- **Incorrect PCR cycling parameters and/or excessive amplification**. Be sure to strictly follow the PCR steps as described in our [CUT&Tag Kit Manual](https://www.epicypher.com/resources/protocols/cutana-cut-and-tag-kit-manual) and [DIY Protocol](https://www.epicypher.com/resources/protocols/cutana-pag-tn5-resources/). The PCR parameters outlined are optimized for 200-700 bp fragments and should eliminate large fragments. If the PCR parameters are correct, but you are still enrichinig large fragments, repeat the CUT&Tag assay using fewer PCR cycles.