Hi! I have posted this question here as well, without answer: http://seqanswers.com/forums/showthread.php?t=39978 If this is my command to Cuffdiff: cuffdiff -o path genes.gtf --labels pre,post bam1.bam,bam2.bam bam2.bam,bam3.bam The "labels" option only names the conditions, here two, "pre" and "post", which both have two BAMs each. Im wondering how to name the BAMs themselves? If this is not possible, can someone explain the organisation of the "read_group_tracking" - files from Cuffdiff. In the column "replicate" is a number corresponding to the BAMs which was input. But the organisation is odd, as you can see: replicate 1 0 2 3 4 6 5 7 8 18 16 9 10 11 12 13 14 15 17 19 20 21 22 23