I have lots of samples that have been aligned to mm10 using RNA STAR. I have successfully assembled transcripts and merge the assembly for all samples using cufflinks. Although Cuffdiff has also worked I would to analyze data with a different statistical test that is not limited to pairwise comparisons. So, I would like to get a table similar to the "transcripts FPKM tracking" output of cudiff but, instead of having only the average for each group of replicates, I would like to have the FPKM value for each replicate. This table will then be analysed for splicing differences, so ideally the table should show fpkm values for isoforms of each gene.