Question: The giant different FPKM value of same gene between cufflink and cuffdiff.
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gravatar for jlzheng
5 weeks ago by
jlzheng0
jlzheng0 wrote:

It differs a lot (10 times as large) between cufflink outputs "gene_FPKM tracking" and cuffdiff outputs"gene differential expression testing". Is it normal in such results?

ADD COMMENTlink modified 4 weeks ago by Jennifer Hillman Jackson24k • written 5 weeks ago by jlzheng0
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gravatar for Jennifer Hillman Jackson
4 weeks ago by
United States
Jennifer Hillman Jackson24k wrote:

Hello,

Yes, the values will be different. Cufflinks calculates statistics based on a single BAM input (sample, replicate) where Cuffdiff utilizes two or more.

The details are included here (summary) and in the linked publication (full algorithm): http://cole-trapnell-lab.github.io/cufflinks/getting_started/#common-uses-of-the-cufflinks-package

Related Q&A: https://biostar.usegalaxy.org/p/4683/#23418

Hope that helps! Jen, Galaxy team

ADD COMMENTlink modified 4 weeks ago • written 4 weeks ago by Jennifer Hillman Jackson24k
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