Read groups RNA-seq and hisat2

Question

[frarodmar17]

I have performed hisat2 alignment on paired-end sequencing data (two separate files: R1 and R2), but output is causing me troubles to perform MarkDuplicates because hisat2 output does not have "read groups". Can I assign a new read group for each hisat2 output? Each hisat2 output is related to one specific sample.

[rfran010]

I don't think read groups should cause a problem. What's the issue you are having?