Hi, I ran CuffDiff using genecode.v25annotation.gtf (downloaded from Gencode) as transcript GTF file. However when I look at the outputs, all the following files are empty:
The remaining output files appear to be fine. Could someone please kindly tell me what I am doing wrong? I thought it might be the genecode .gtf file but after looking at it and looking at similar files used by other people to do similar analysis the file seems fine.
Thanks to anyone who can help me with this. Manu