Hope someone can help,
I have some RNASeq data and I have 2 groups (Control and Treatment) each containing 3 replicates. When I run Cuffdiff just as proof of concept I ran the groups (Control and Treatment) with one sample in each group. This worked great, the gene names were assigned and there were values present for log2(fold_change) everything looked good. Now, when I add my replicates to each respective group 3 Control against 3 Treatment Cuffdiff produces zeros across the board, no log2 fold change, no FPKM....I still get the gene names but it's as if Cuffdiff couldn't perform any calculations. Please don't say this is an issue with my GTF file matching my genome FASTA because these files work perfectly when only using 1 sample per group. Please help if you have any advice.