Question: Difference of FPKM between cufflink and cuffdiff
0
gravatar for cfarmeri
3.8 years ago by
cfarmeri150
Japan
cfarmeri150 wrote:

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 wondering which i should use for the purpose of comparing gene expression

difference between two samples.

Please help me ...Thanks!!

 

 

 

rna-seq • 4.0k views
ADD COMMENTlink modified 3.6 years ago by rodolpho.gheleri50 • written 3.8 years ago by cfarmeri150
3
gravatar for rodolpho.gheleri
3.6 years ago by
Brazil
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.

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

ADD COMMENTlink written 3.6 years ago by rodolpho.gheleri50
1

so cool,,,thanks!!
 

ADD REPLYlink written 3.6 years ago by cfarmeri150

What a really nice answer!

ADD REPLYlink written 9 months ago by dhkwnr950
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