Hi, I am a new comer of the forum. I tried to find out the answer to a question about FPKM in the pipeline Tophat/Cufflinks but I failed. So I post the question here, hoping someone might give me some hints.
Recently our lab did a RNA-seq studies on the transcriptome of plant. I successfully applied the Tophat/Cufflinks pipeline analysis to our RNA-seq data. I used Tophat v2.0.8 and Cufflinks v2.0.2. I followed the steps listed in the Nature Protocols paper of Trapnell exactly.
I wanted to calculate the FPKM for each gene under different conditions. So I checked the genes.fpkm_tracking output of the cuffmerge and the genes.fpkm_trancking output of the cuffdiff (after cuffmerge command). However, I found out that the FPKM values in these two files differed (e.g., 4.94066e-324 vs. 31.2836).
How could I interpret this result?
Any advices are welcome. Thanks.
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