---
title: "Summary of ATAC-seq quality control and success metrics"
slug: "summary-of-atac-seq-quality-control-and-success-metrics"
status: "new"
updated: 2026-09-15T01:28:10Z
published: 2026-09-15T01:28:10Z
canonical: "support.epicypher.com/summary-of-atac-seq-quality-control-and-success-metrics"
---

> ## 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.

# Summary of ATAC-seq quality control and success metrics

The CUTANA ATAC-seq Kit provides multiple quality control checks to ensure consistent generation of robust open chromatin profiles (**Figure 1** and **Figure 2**), including established ATAC-seq success metrics, to support reliable ATAC-seq workflows [1]. To assess ATAC-seq library quality based on enrichment of accessibility signals around Transcription Start Sites (TSSs), calculate the TSS enrichment score according to [ENCODE recommendations](https://www.encodeproject.org/atac-seq/) as a functional signal-to-background measure.

![](https://cdn.document360.io/1fc69f91-cf1e-45ab-bc51-4063eb80e37c/Images/Documentation/Figure 4 ATAC-seq Manual [success and opt table].jpg)

**Figure** **1.** Success metrics and optimization guidelines.

![](https://cdn.document360.io/1fc69f91-cf1e-45ab-bc51-4063eb80e37c/Images/Documentation/image(25).png)

F**igure 2.** Representative open chromatin profiles and QC metrics generated by a robust, well-established ATAC-seq workflow. Results demonstrate highly reproducible peak profiles, strong FRiP scores, and high TSS enrichment across experiments