Hi All I recently ran cufflinks-cuffmerge-cuffdiff for my RNA-seq dataset. When I checked the isoforms.fpkm.tracking, I noticed = and j class codes. I passed the reference gtf with -g option when running cuffmerge. When I checked similar results for a different dataset I only saw '=' classcode in the file (although I used cuffcompare instead of cuffmerge for these runs). I am wondering if there's anything I might be doing wrong. Any help is appreciated.

Thanks.