---
title: "What does the CUTANA™ CUT&RUN/Tag pipeline do?"
slug: "what-does-the-cutana-cutruntag-pipeline-do"
updated: 2026-11-13T17:06:01Z
published: 2025-08-27T15:43:59Z
canonical: "support.epicypher.com/what-does-the-cutana-cutruntag-pipeline-do"
---

> ## 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 does the CUTANA™ CUT&RUN/Tag pipeline do?

The CUTANA™ CUT&RUN/Tag Alignment Pipeline processes paired-end FASTQ files by aligning reads to a designated reference genome. During this process, reads that can align to more than one location in the reference genome (multi-aligned reads) are discarded. By default reads with identical sequences that align to a single location (duplicates) as well as reads aligning to regions of the genome known to give false-positives (ENCODE DAC Exclusion List) are discarded as well. However, removing duplicates and reads aligned to the Exclusion List is optional, and can be turned off in the Advanced Settings menu during the New Alignment workflow.

Optionally, the pipeline can concurrently analyze CUTANA™ Spike-in Controls and align to the *E. coli* reference genome, as specified when entering Reaction Details. Supported reference genomes include human (hg19, hg38, T2T-CHM13v2.0), mouse (mm10), Drosophila (dm6), and yeast (sacCer3).