cuffdiff notest but cufflinks shows fpkm > 10

Question

[urmi208]

Hello,

I have encountered a problem with cuffdiff and thought you might be able to help.

I am trying to do alternative splicing differential expression analysis using cuffdiff. I have followed tuxedo pipeline as published in the paper but in cuffdiff output, the entry for test-status is "NOTEST" for almost all transcripts, which means the test wasn't performed because there isn't ample data. This is not true, we have a lot of data which is seen in cufflinks results. (There are a lot of entries with fpkm > 10)

I have tried a lot of things to get this working but no luck

Thanks for any help you can provide.