I ran cuffdiff using Refseq genes as GTF and two groups of BAM. Group
one has two replicates (treated) and group two only one replicate

When looking at the outputs the following are empty (1 line):

TSS group FPKM tracking
TSS groups differential expression testing
CDS FPKM tracking
CDS FPKM differential expression testing
CDS overloading diffential expression testing
promoters differential expression testing
splicing differential expression testing

the other four outputs have data downloadable as excel.

Is this normal?

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