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!