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!
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.
I am having the same problem: When I select HiSat2 as the analysis that produced the output files, my HiSat2 files are not selectable options to run the MultiQC.
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:
