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Hello,
I am using galaxy to do some simple tophat/cufflinks analysis of RNA-Seq to the bovine genome. When I run 2 different samples through tophat and cufflinks I get gene lists with FPKMs per normal. However when I run the alignments from the two samples through cuffdiff the value 1 and value 2 do not match the FPKM values for the same transcript from the separate cufflinks values. I need these to match if I am using gene lists from cufflinks for some analysis. Without them matching I am concerned that I could be missing some significantly differentially expressed transcripts because it is not even using the FPKM values from cufflinks output. Is there a reason these FPKM values are not matching? Is there a way to get it so they do match so I can accurately analyze my data using Cufflinks and Cuffdiff results together? I am not much for coding so I would really like to get this working through galaxy or some other option. Is this a known problem or is this accurate because of some sort of differential analysis methods between Cufflinks and Cuffdiff? Thank you in advance for any help on the matter.
I am using galaxy to do some simple tophat/cufflinks analysis of RNA-Seq to the bovine genome. When I run 2 different samples through tophat and cufflinks I get gene lists with FPKMs per normal. However when I run the alignments from the two samples through cuffdiff the value 1 and value 2 do not match the FPKM values for the same transcript from the separate cufflinks values. I need these to match if I am using gene lists from cufflinks for some analysis. Without them matching I am concerned that I could be missing some significantly differentially expressed transcripts because it is not even using the FPKM values from cufflinks output. Is there a reason these FPKM values are not matching? Is there a way to get it so they do match so I can accurately analyze my data using Cufflinks and Cuffdiff results together? I am not much for coding so I would really like to get this working through galaxy or some other option. Is this a known problem or is this accurate because of some sort of differential analysis methods between Cufflinks and Cuffdiff? Thank you in advance for any help on the matter.
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