Entering edit mode
10.6 years ago
pm2013
▴
50
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.
What would happen if you ran the exact same pipeline? Effectively, you ran different pipelines, got different results then ask 'what have I done wrong?'. Please try and compare like with like and let us know what changes.