Hi all,

  So I am using cuffdiff to find significant differences between two samples (no replicates).  The transcript and gene differential expression works and I get significant values.  However, consistently, the TSS, CDS, and splicing differences return with "1 line" and no data.  I have tried multiple different GTF transcriptome reference files  - UCSC refflat, ensembl, but still no luck. 

  Maybe I am missing something very basic - can anyone give me advice here?

Richard