Hello, I am using the Galaxy tool Cuffdiff to analyze the RNA-seq data. But for the output file "genes.fpkm_tracking", I found there are redundant genes, I mean the same gene short name, but with different tracking IDs, different gene IDs and different locus. Could you please tell me why this happen? And what's the difference between tracking IDs and gene IDs?
Thank you very much for your help. Looking forward to your reply.