I ran cuffdiff using c.elegans( WBcel235) gtf file on two groups of bam, ech having three replicates. The output produced by cuffdiff had empty cds.diff, cds.count_tracking and cds.fpkm_tracking. I have checked several sites regarding this issue and found that, the gtf file suppied should contain tss_id and p_id attributes. However, I re-ran cuffdiff with gtf file having both the attributes and again the outputs of cds files were empty. Other outputs seemed normal.
Can anyone help me with this?