---
title: "My CUT&Tag library is enriched for fragments ~100 bp. What does this mean?"
slug: "cut-and-tag-small-fragments"
updated: 2025-07-15T14:42:34Z
published: 2025-07-15T14:42:34Z
canonical: "support.epicypher.com/cut-and-tag-small-fragments"
---

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# My CUT&Tag library is enriched for fragments ~100 bp. What does this mean?

Fragments between 25 and 100 bp are likely primer dimers (**Figure 1**), which occur when indexing PCR primers preferentially self-ligate. Enrichment of primer dimers often indicates problems with tagmentation efficiency and/or PCR amplification, and are most common when performing CUT&Tag with low numbers of nuclei.

If primer dimers comprise >5% of the library, additional cleanup should be performed prior to sequencing. We recommend performing cleanup on pooled libraries, not individual libraries, to minimize sample loss. Use the bead:DNA ratios suggested in the Application Notes for our CUTANA™ DNA Purification Beads ([EpiCypher 21-1407](http://www.epicypher.com/product/cutana-dna-purification-beads/)) for maximal recovery.

![](https://cdn.document360.io/1fc69f91-cf1e-45ab-bc51-4063eb80e37c/Images/Documentation/Primer Dimers CUT&Tag@2x.png)

**Figure 1:** TapeStation trace for CUTANA CUT&Tag library targeting H3K4me3 shows a small amount of primer dimer contamination (~75 bp). However, the library is primarily enriched for mononucleosome-sized fragments (~300 bp), and does not require additional cleanup prior to sequencing.