Class Codes After Cuffmerge
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9.4 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.

cuffmerge cufflinks rna-seq • 3.2k views
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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.

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