I was trying to comparing multiple RNA-Seq samples using cuffdiff. However, it is difficult to visualize the FPKM and log2 fold change output file. For example, I have 3 samples A, B, and C. When I look at gene X, I have 3 rows listing the results of A vs B, B vs C, and A vs C.
Is there a way to merge that 3 rows into 1? A vs B vs C? Or which software can achieve that?