# Attempting to use MultiQC to visualize alignment with HISAT2 but the HISAT2 output collection does not appear

**URL:** <https://help.galaxyproject.org/t/attempting-to-use-multiqc-to-visualize-alignment-with-hisat2-but-the-hisat2-output-collection-does-not-appear/5141>\
**Category:** usegalaxy.org support\
**Tags:** multiqc, collections\
**Created:** [January 5, 2021, 8:43pm UTC](https://help.galaxyproject.org/t/attempting-to-use-multiqc-to-visualize-alignment-with-hisat2-but-the-hisat2-output-collection-does-not-appear/5141 "2021-01-05T20:43:19Z")\
**Posts on this page:** 1\
**Showing post:** 5

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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:** [August 24, 2021, 5:49pm UTC](https://help.galaxyproject.org/t/attempting-to-use-multiqc-to-visualize-alignment-with-hisat2-but-the-hisat2-output-collection-does-not-appear/5141/5 "2021-08-24T17:49:26Z")

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Hello @rmwade1786 @ypo @StefaniaMontesinos

Please see this prior Q&A:

> [@Hisat2 BAM file output does not include stats -- Not a default output but is an option on the tool form](https://help.galaxyproject.org/t/hisat2-bam-file-output-does-not-include-stats-not-a-default-output-but-is-an-option-on-the-tool-form/3764/2):
>
> To output statistics directly from `HISAT2` , that output option needs to be set to “Yes” on the tool form. Find it nested under the section “Summary Options”. This would allow you to use `MultiQC` to compare multiple BAM results together in a single report.
> 
> ![hisat2-output-alignment-stats](https://us1.discourse-cdn.com/flex020/uploads/galaxy/original/2X/3/31fad0bc77ed62993b477df729739e4a6efff752.png)

Galaxy has had some interface style updates since the original post, but the optional output toggle is still in the same place on the tool form, and will look like this:

 ![hisat2-summary-output-toggle-for-multiqc](https://us1.discourse-cdn.com/flex020/uploads/galaxy/original/2X/d/d347859633cb25a681dd9a484827cf3011a8dc9f.png)

Hope that helps everyone!

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_[View the full topic](https://help.galaxyproject.org/t/attempting-to-use-multiqc-to-visualize-alignment-with-hisat2-but-the-hisat2-output-collection-does-not-appear/5141)._