Question

Difference of FPKM between cufflink and cuffdiff

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9.5 years ago

cfarmeri ▴ 210

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!

RNA-Seq • 6.9k views

ADD COMMENT • link updated 2.1 years ago by Ram 44k • written 9.5 years ago by cfarmeri ▴ 210

Ram · Answer 1 · 2015-07-31

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9.3 years ago

rodolpho.gheleri ▴ 60

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 COMMENT • link updated 2.1 years ago by Ram 44k • written 9.3 years ago by rodolpho.gheleri ▴ 60

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So cool, thanks!

ADD REPLY • link updated 2.1 years ago by Ram 44k • written 9.3 years ago by cfarmeri ▴ 210

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What a really nice answer!

ADD REPLY • link 6.5 years ago by dhkwnr95 ▴ 20