Cuffdiff Output/Cummerbund

Question

[Kaustubh]

Hi everyone,

I want to analyze data using cummeRbund but I'm having problem with cuffdiff output. I don't get any entries in the geneid and gene columns in the output files of cuffdiff. Also all the other files except isoformexp.diff, isoform.FPKM_tracking are blank. When I specify file into the cummeRbund, I get following output, {CuffSet instance with: 2 samples 0 genes 0 isoforms 0 TSS 0 CDS 0 promoters 0 splicing 0 relCDS} What might be the problem here? I would really appreciate any help in this regard. Thanks in advance!

[A. Domingues]

This is a bit late but I'm having the same problem using SE data without replicates.