# How do you use MultiQC on FastQC files taken from SRA files?

**URL:** <https://help.galaxyproject.org/t/how-do-you-use-multiqc-on-fastqc-files-taken-from-sra-files/169>\
**Category:** usegalaxy.org support\
**Tags:** multiqc, quality-control\
**Created:** [December 9, 2018, 7:04pm UTC](https://help.galaxyproject.org/t/how-do-you-use-multiqc-on-fastqc-files-taken-from-sra-files/169 "2018-12-09T19:04:49Z")\
**Posts on this page:** 1\
**Showing post:** 2

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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:** [December 10, 2018, 4:06pm UTC](https://help.galaxyproject.org/t/how-do-you-use-multiqc-on-fastqc-files-taken-from-sra-files/169/2 "2018-12-10T16:06:07Z")

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XREf → [multQC issue and guidance? - #2 by jennaj](https://help.galaxyproject.org/t/multqc-issue-and-guidance/14914/2)

Please see this tutorial [Manipulating NGS data with Galaxy - Galaxy Community Hub](https://galaxyproject.org/tutorials/ngs/#organizing-and-qcing-multiple-datasets) for:

- How to create fastq dataset collections
- How to run FastQC in batch on collections
- How to generate a MultiQC report based on those FastQC results in a collection

**Double checks:** Make sure the MultiQC tool form is set up correctly for this use case (all covered by the video in the tutorial):

1. FastQC reports are in a dataset collection
2. “FastQC” is set as the report type.
3. “Dataset Collections” are set as the input type.
4. Pick the “raw” results (text report). The “html” results are not appropriate.

My guess is that either item 2 or 3 was not set properly on the FastQC tool form.

`admin edit: Cross-posted at Gitter:` [https://gitter.im/galaxyproject/Lobby?at=5c0c5f88178d7860a1a84938](https://gitter.im/galaxyproject/Lobby?at=5c0c5f88178d7860a1a84938)

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