Difference of FPKM between cufflink and cuffdiff

Question

[cfarmeri]

Hi

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'm wondering which I should use for the purpose of comparing gene expression difference between two samples.

Please help me. Thanks!

Answer 1

[rodolpho.gheleri]

Yes, it's because the "Library Normalization Methods" used by default for each one. Meanwhile cufflinks use classic-fpkm normalization, the cuffdiff default is geometric. Please check the section "Library Normalization Methods" in the link below. To change the method when you run cuffdiff, type --library-norm-method classic-fpkm in options.

Source: http://cole-trapnell-lab.github.io/cufflinks/cuffdiff/index.html#library-types

[cfarmeri]

So cool, thanks!

[dhkwnr95]

What a really nice answer!