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!
1 answer
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
•
written
by
rodolpho.gheleri •
What a really nice answer!
Log in to answer this question.
-
Calculate TPM from cuffnorm count data
written by galozs •
-
No differential gene expression after tuxedo protocol
written by vinayjrao
-
Doubts about RNA-seq Cufflinks
written by vm.higareda •
-
RNA-seq: Comparing 2 strains (same experimental conditions)
written by Cricket •
-
Two FPKM values for same gene
written by Bioblazer
-
Pairwise Cuffdiff Usage
written by cfarmeri
-
Differential Expression Two References One Condition
written by MiguelMorard •
-
How to handle technical and biological replicates using cufflinks
written by ejmcmaho •
-
tophat-cufflinks command pipeline
written by biolab
-
Cufflinks And Cuffdiff Fpkm Values In Galaxy
written by KS
