# Do these data require trimming/preprocessing?

**URL:** <https://help.galaxyproject.org/t/do-these-data-require-trimming-preprocessing/18140>\
**Category:** usegalaxy.org support\
**Tags:** quality-control\
**Created:** [July 2, 2026, 8:50pm UTC](https://help.galaxyproject.org/t/do-these-data-require-trimming-preprocessing/18140 "2026-07-02T20:50:17Z")\
**Posts on this page:** 3\
**Page:** 1

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**Author:** ![09303030076](https://avatars.discourse-cdn.com/v4/letter/0/7cd45c/32.png) [@09303030076](https://help.galaxyproject.org/u/09303030076)\
**Post date:** [July 2, 2026, 8:50pm UTC](https://help.galaxyproject.org/t/do-these-data-require-trimming-preprocessing/18140/1 "2026-07-02T20:50:17Z")

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Hi everyone

I’m working with these samples in **Galaxy** and just generated this **MultiQC** report. Based on the status checks, I have a few questions:

1. Do these data require **trimming/preprocessing**?
2. Which tool would you recommend for trimming within the Galaxy environment? Should I go with **fastp** , **Trimmomatic** , or **Cutadapt**?

I’d appreciate your insights on the best workflow to clean up these reads before downstream analysis.

Best regards

 ![1](https://us1.discourse-cdn.com/flex020/uploads/galaxy/original/2X/6/6842ab0e4b3c6476607e1b547a886f79134eadcc.png)

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**Author:** ![wm75](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/wm75/32/56_2.png) [@wm75](https://help.galaxyproject.org/u/wm75)\
**Post date:** [July 3, 2026, 10:07am UTC](https://help.galaxyproject.org/t/do-these-data-require-trimming-preprocessing/18140/2 "2026-07-03T10:07:03Z")

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Hi,

1. likely yes
2. cutadapt is good and very powerful choice with many options. For standard cases there’s nothing wrong with trimmomatic either. fastp is different in that it does QC and trimming in one → it’s particularly useful if you’re repeatedly generating data via the same wetlab protocol and you want to standardize trimming anyway, i.e. you only want to inspect the QC reports afterwards as an extra control step, but you’re not regularly basing your preprocessing decision on the QC outcome.

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<div class="post-metadata">

**Author:** ![09303030076](https://avatars.discourse-cdn.com/v4/letter/0/7cd45c/32.png) [@09303030076](https://help.galaxyproject.org/u/09303030076)\
**Post date:** [July 5, 2026, 11:21am UTC](https://help.galaxyproject.org/t/do-these-data-require-trimming-preprocessing/18140/3 "2026-07-05T11:21:53Z")

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“My data consists of RNA-seq reads. Given that both the ‘adapter content’ and ‘per base sequence quality’ metrics are completely green in FastQC, is trimming still necessary?”

“In cases where the quality metrics do not explicitly require trimming, could applying Cutadapt potentially introduce any issues or adverse effects, or is it considered a safe practice?”