I would like to find out whether there are any changes in major isoform (most expressed) per gene in my time course experiment. I can get this information by parsing FPKM values from cufflinks.
Do you know of any more sophisticated tool/method capable of identifying major isoform changes between conditions?
EDIT: I've ended up writing my own script. Details in here.
EDIT2: fpkm2major.py can be downloaded from my github