I am trying to adapt the HISAT2 options to my samples and I encountered this problem:
I know what I want: I don’t want HISAT2 to try and align individual mates.
So I should add the command --no mixed behaviour.
But what this means in Galaxy? Yes or No?
It basically says: HISAT2 does this. By default is False (no-mixed). Do you want for No-mixed behaviour to be disabled? Y/N.
It sounds like I am disabling the button that disables? Is Galaxy using the default settings for HISAT2 (and other programs)? Or it comes with its own recommendations?
I am not sure what Yes and No mean in this context. Am I reading too much into this?