---
title: "How do I trim my FASTQ files?"
slug: "how-do-i-trim-my-fastq-files"
updated: 2025-08-27T15:43:32Z
published: 2025-08-27T15:43:32Z
canonical: "support.epicypher.com/how-do-i-trim-my-fastq-files"
---

> ## 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.

# How do I trim my FASTQ files?

For paired-end FASTQ files exceeding 50 bp, a crucial preprocessing step may be required to ensure compatibility with the CUTANA Cloud Experiment platform. This involves adjusting the read lengths to meet the specified requirements. Tools such as [Trimmomatic](https://github.com/usadellab/Trimmomatic) and [Trim Galore](https://github.com/FelixKrueger/TrimGalore) are recommended for this purpose.

For a simple approach, files can be cropped to a length of 50 bases. For more advanced application of the tools, adapter sequences can be detected and removed. Failure to trim adapter sequences will prevent reads from aligning to the reference genome and result in a reduction in overall unique alignment rate.

  

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