Hi all,
  So I am using cuffdiff to find significant differences between two samples 
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?

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