Hi - hope everyone is holding up in these days!
I am doing RNA-seq analysis on some plant data (over different time points) and ran tophat then cuffdiff (following Trapnell et al 2012 Nature paper protocol). However for all of my comparisons (e.g. september vs november; november vs january; february vs march) my gene_exp.diff file has only one gene listed whereas the isoform_exp.diff file has thousands. I assume this means the analysis failed (there is no way there aren't genes deferentially expressed during these different time points).
I'm also trying to work out what genes are what using GO term analysis - does anyone know how to upload file list of genes from my cuffdiff output? At the moment I am doing it manually which I now realise is ridiculous...
Thank you so much for your helps!