Read groups RNA-seq and hisat2
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.
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frarodmar17 •
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I don't think read groups should cause a problem. What's the issue you are having?