---
title: "Do I need to trim my FASTQ files?"
slug: "do-i-need-to-trim-my-fastq-files"
updated: 2025-08-27T15:43:28Z
published: 2025-08-27T15:43:28Z
canonical: "support.epicypher.com/do-i-need-to-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.

# Do I need to trim my FASTQ files?

CUT&RUN and CUT&Tag typically produce a distribution of insert sizes around 150 bp (footprint of a nucleosome), while some transcription factors are known to produce sub-150 bp fragments, but these are less common. As such,

**2x150 bp sequencing:** Yes, you should trim adapter sequences prior to upload. A significant number of genomic fragments will be <150 bp, meaning the sequencing reads will contain adapter sequences and fail to align, reducing your overall alignment rate.

**2x100 bp sequencing:** No, unless you are mapping a transcription factor that produces sub-nucleosomal fragments (<250 bp as seen by TapeStation after the multiplexing PCR). If your library contains small fragments you should trim. **2x50 bp sequencing:** No, you do not need to trim.