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Question: The giant different FPKM value of same gene between cufflink and cuffdiff.
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10 months ago by
jlzheng • 0
jlzheng • 0 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?
rna-seq cufflinks fpkm expression cuffdiff • 388 views
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modified 10 months ago by Jennifer Hillman Jackson ♦ 25k • written 10 months ago by jlzheng • 0
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gravatar for Jennifer Hillman Jackson
10 months ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k 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 COMMENT • link modified 10 months ago • written 10 months ago by Jennifer Hillman Jackson ♦ 25k
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