---
title: "What is the difference between a FASTQ and a reaction?"
slug: "what-is-the-difference-between-a-fastq-and-a-reaction"
updated: 2025-08-27T15:43:42Z
published: 2025-08-27T15:43:42Z
canonical: "support.epicypher.com/what-is-the-difference-between-a-fastq-and-a-reaction"
---

> ## Documentation Index
> Fetch the complete documentation index at: https://support.epicypher.com/llms.txt
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# What is the difference between a FASTQ and a reaction?

The CUTANATM CUT&RUN/Tag alignment pipeline requires sequencing libraries generated from paired-end sequencing to efficiently map reads back to the reference genome. Therefore, there should be two (2) FASTQ files for every reaction of CUT&RUN. On the platform, a Reaction is identified by its FASTQ Prefix, the portion of the FASTQ filename that is shared by only the forward and reverse read field (R1 & R2).