What does Cuffdiff do?

The cutdiff function finds any significant changes in transcript expression, splicing, and promoter use (Trapnell et al., 2010). Cuttdiff is an algorithm for transcript assembly that uses a statistical model to produce estimates of isoforms (functionally similar proteins with different amino acids) abundances.

Where we compare the abundances of 2 samples and tell us which RNA reads are different. Ultimately gives us differential expression.

References: Trapnell C. et al., 2010. Transcript assembly and quantification by RNA-Seq revels annotated transcripts and isoform switching during cell differentiation. Nat Biotechnol. 28(5):511-515. doi:10.1038/nbt.1621