When using the -G option in TopHat/Cufflinks, the manual states that the "Output will include all reference transcripts as well as any novel genes and isoforms that are assembled."
Where can I see these novel genes or the expression data for them? They don't seem to be reported...
Do I need to use another option or carry out further processing prior to using CuffDiff? I don't think I can use cuffmerge as it doesn't generate GTF files for each replicate when using the -G option.