# 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:** 2\
**Page:** 1

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**Author:** ![Ben\_Oppenheimer](https://avatars.discourse-cdn.com/v4/letter/b/8e8cbc/32.png) [@Ben\_Oppenheimer](https://help.galaxyproject.org/u/Ben_Oppenheimer)\
**Post date:** [December 9, 2018, 7:04pm UTC](https://help.galaxyproject.org/t/how-do-you-use-multiqc-on-fastqc-files-taken-from-sra-files/169/1 "2018-12-09T19:04:49Z")

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I am new to Galaxy and bioinformatics so feel free to let me know if there is a better way of asking my question. The files were executed in a way that the MultiQC did not recognize the files existed. I downloaded SRA files to Galaxy. These files were transfered to a Paired-end data folder with each accession (sample) inside along with the forward and reverse fastq files. This general file format remains after running these Files through FastQC. Now, I am trying to run the files through MultiQC but the data is not recognized. Does anyone have suggestions on how to fix this?

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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)