I am running an analysis in CuffDiff using a GFF file of annotations from FlyBase www.flybase.org). The GFF file contains annotation data for genes, mRNA, CDS and 5'- and 3'-UTR's.
Differential expression of isoforms is reported in some 1266 pairwise comparisons. However, most of the genes in the analysis contain only 1 transcript; and there is very little overlap between the genes showing differential expression (file gene_exp.diff) and the isoforms showing differential expression (file isoform_exp.diff). Can any one explain to me how this is possible?