Question: Difference of FPKM between cufflink and cuffdiff
gravatar for cfarmeri
5.2 years ago by
cfarmeri160 wrote:



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!!




rna-seq • 5.1k views
ADD COMMENTlink modified 5.0 years ago by rodolpho.gheleri50 • written 5.2 years ago by cfarmeri160
gravatar for rodolpho.gheleri
5.0 years ago by
rodolpho.gheleri50 wrote:

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.


ADD COMMENTlink written 5.0 years ago by rodolpho.gheleri50

so cool,,,thanks!!

ADD REPLYlink written 5.0 years ago by cfarmeri160

What a really nice answer!

ADD REPLYlink written 2.2 years ago by dhkwnr950
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