Differential Isoform Expression In Cuffdiff: How Does It Work?

Question

[gwilymh1000]

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?

[GANI]

Do you mean to say that there are 1266 transcripts that are significant? How many genes are significant in the same comparison? It will be good if you can provide some sample data (the isoforms/genes)