adding read group information when multiple FASTQ pairs are provided

[jmlivingstone]

How do I add read group information per FASTQ pair when more than one FASTQ pair is provided?

I tried this but it doesn't split the read group information --rg-id=RGID1,RGID2 --rg CN:CN,CN --rg LB:LB,LB --rg PL:PL,PL --rg PU:PU,PU -1 test_R1.fastq.gz,test_R1_L2.fastq.gz -2 test_R2.fastq.gz,test_R2_L2.fastq.gz so all entries have RG:Z:RGID1,RGID2 and the header has @RG ID:RGID1,RGID2 CN:CN,CN LB:LB,LB PL:PL,PL PU:PU,PU

[parkchanhee]

@jmlivingstone HISAT2 can set only one read group id per a SAM file. You can also run HISAT2 separately with a different rg-id and merge them into one file.