# FastQC fails with Trimmomatic trimmed, unpaired reads

**URL:** <https://help.galaxyproject.org/t/fastqc-fails-with-trimmomatic-trimmed-unpaired-reads/6553>\
**Category:** usegalaxy.org support\
**Created:** [August 19, 2021, 10:16pm UTC](https://help.galaxyproject.org/t/fastqc-fails-with-trimmomatic-trimmed-unpaired-reads/6553 "2021-08-19T22:16:40Z")\
**Posts on this page:** 1\
**Page:** 1

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**Author:** ![rmwade1786](https://avatars.discourse-cdn.com/v4/letter/r/7993a0/32.png) [@rmwade1786](https://help.galaxyproject.org/u/rmwade1786)\
**Post date:** [August 19, 2021, 10:16pm UTC](https://help.galaxyproject.org/t/fastqc-fails-with-trimmomatic-trimmed-unpaired-reads/6553/1 "2021-08-19T22:16:40Z")

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Hello,

I am trying to compare the output files of Trimmomatic using FastQC and ultimately MultiQC. FastQC is able to assess the trimmed, paired reads, but not the trimmed unpaired reads; I have tried several times, and the runs fail every time. Is there a reason why this shouldn’t work? In the past, it has seemed that Trimmomatic works better with unpaired reads, but I would like to prove this by looking at the quality statistics.

Thank you for your help!

Rachael