I've been trying to analyse an RNA-seq dataset, and I decided to try the newer HISAT2>StringTie>Ballgown approach instead of Tophat2>Cufflinks>CummeRbund etc.
I'm having real trouble working out how to handle my biological replicates, as there doesn't seem to be much documentation or discussion on these newer tools. It seems like most people would use Cuffnorm and it's easy to see why as you can very easily specify what are your repeats for each sample. I'm sure there's a way to do this in Ballgown but I'm far to inexperienced to spot it so any help would be fantastic.
Thanks in advance.