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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