# .fastq.gz dataset not showing up in fastqc

**URL:** <https://help.galaxyproject.org/t/fastq-gz-dataset-not-showing-up-in-fastqc/13745>\
**Category:** usegalaxy.eu support\
**Tags:** collections\
**Created:** [October 22, 2024, 2:33pm UTC](https://help.galaxyproject.org/t/fastq-gz-dataset-not-showing-up-in-fastqc/13745 "2024-10-22T14:33:19Z")\
**Posts on this page:** 5\
**Page:** 1

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**Author:** ![oliverb12](https://avatars.discourse-cdn.com/v4/letter/o/e68b1a/32.png) [@oliverb12](https://help.galaxyproject.org/u/oliverb12)\
**Post date:** [October 22, 2024, 2:33pm UTC](https://help.galaxyproject.org/t/fastq-gz-dataset-not-showing-up-in-fastqc/13745/1 "2024-10-22T14:33:19Z")

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Hi all, I have a dataset that is comprised of data that I have processed with fastp - all in .fastq.gz format. However, when I select a dataset to use on fastqc my other datasets show up (i.e. the original data and trimmed data) but not the fastp processing output. Any ideas as to why this could be?

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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:** [October 22, 2024, 3:31pm UTC](https://help.galaxyproject.org/t/fastq-gz-dataset-not-showing-up-in-fastqc/13745/2 "2024-10-22T15:31:48Z")

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Hi,  
when you’re saying your _trimmed_ data shows up, what’s that then (if not the fastp output)?

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**Author:** ![oliverb12](https://avatars.discourse-cdn.com/v4/letter/o/e68b1a/32.png) [@oliverb12](https://help.galaxyproject.org/u/oliverb12)\
**Post date:** [October 22, 2024, 8:55pm UTC](https://help.galaxyproject.org/t/fastq-gz-dataset-not-showing-up-in-fastqc/13745/3 "2024-10-22T20:55:32Z")

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Hi,  
It was trimmed using porechop and then that was subsequently processed with fastp.

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**Author:** ![jennaj](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/jennaj/32/27_2.png) [@jennaj](https://help.galaxyproject.org/u/jennaj)\
**Post date:** [October 28, 2024, 11:58pm UTC](https://help.galaxyproject.org/t/fastq-gz-dataset-not-showing-up-in-fastqc/13745/4 "2024-10-28T23:58:49Z")

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HI @oliverb12

It sounds like you have fastq data as the output from fastp but the _shape_ of that data is not matching up with the FastQC tool form.

By “shape” I mean how it is organized. Is it inside a collection? A paired end collection? Individual files? Try to organize your data to match how the tool form is looking for inputs (or the reverse). This will probably solve your problem, and if you need to change the shape, maybe from a nested paired end collection to something simple like two lists (one forward, one reverse), go into the Collection Operations section of the tool panel and you will find ways to do this.

Please ask if you get stuck, and we can probably help more with specific tool choices. We will need to know what you have now, the exact tool you plan to use. That can be with screenshots or a shared history link. See the banner at this forum for how to share your work if that is how you would prefer to share (tends to be faster, and leads to less confusion, question → straight to actionable advice).

Thanks, and let us know how this worked out! 🙂

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**Author:** ![oliverb12](https://avatars.discourse-cdn.com/v4/letter/o/e68b1a/32.png) [@oliverb12](https://help.galaxyproject.org/u/oliverb12)\
**Post date:** [October 30, 2024, 11:40am UTC](https://help.galaxyproject.org/t/fastq-gz-dataset-not-showing-up-in-fastqc/13745/5 "2024-10-30T11:40:49Z")

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Hi @jennaj

Thanks so much for the response, I did manage to get it work and it seems that the problem was simply that the dataset was not being recognised as being in the fastqc format so FastQC didn’t want it. I fixed it by changing it from an auto dataset to a fastsanger dataset (oddly the fastqc dataset type didn’t work).

Thank you for the advice though!