i have each rna-seq data of 2 experiment samples.
After mapping through tophat, i tried to compare gene expression difference.
As for respective samples, cufflinks get FPKM of genes to me.
simultaneously, i compared the two samples FPKM by using cuffdiff.
But the FPKM from cufflinks and cuffdiff are not same,
so i wondering which i should use for the purpose of comparing gene expression
difference between two samples.
Please help me ...Thanks!!