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

usegalaxy.org support
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#1

Hello,

I am a new Galaxy user doing my first RNA-seq analysis. I had my data in a collection and aligned it using HISAT2. This generated a collection titled “HISAT2 on …: aligned reads (BAM)” with a list that I then attempted to enter into MultiQC, but the HISAT2 collection does not appear in the option (individual HISAT2 files for each sample can be selected). When I ran HISAT2 tool I had these parameters for output:

Output alignment summary in a more machine-friendly style. True
Print alignment summary to a file. False

Do I need a printed alignment summary in order to be able to run MultiQC?

I would really appreciate any help on this topic, thanks!

#2

Does it appear as a collection?

#3

Individual HISAT2 results that are hidden appear under multiple datasets, but when I select dataset collections the HISAT2 collection containing a list of all the samples does not appear.