Question: What is the difference between gene FPKM and transcript FPKM values?
1
gravatar for Arindam Ghosh
3.0 years ago by
Arindam Ghosh350
Finland
Arindam Ghosh350 wrote:

What is the difference between gene FPKM and transcript FPKM values? Or rather how is FPKM value for gene obtained from FPKM values of transcript. Average is not suitable as only one transcripts may have expression out of several. So what method is used to do so.

rna-seq • 1.8k views
ADD COMMENTlink modified 3.0 years ago • written 3.0 years ago by Arindam Ghosh350
1
gravatar for Arindam Ghosh
3.0 years ago by
Arindam Ghosh350
Finland
Arindam Ghosh350 wrote:

Thak you Seidel for showing the way. I have now been able to find the calculation methods.

The general method for calculation of transcript FPKM is explained here.

As I am using Ballgown tool, I found the answer to my question in supplementary article in one of their papers Ballgown bridges the gap between transcriptome assembly and expression analysis. The gene FPKM vale calulation is explained under the heading Expression data.

ADD COMMENTlink written 3.0 years ago by Arindam Ghosh350
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gravatar for seidel
3.0 years ago by
seidel7.4k
United States
seidel7.4k wrote:

It depends on what software you're using, and what you are actually quantifying. Most people gloss over the issue because transcripts and genes are complicated, and specific choices need to be made in order to be precise about either. Nonetheless, generally philosophically speaking: the output of the gene (the gene FPKM) will be considered the sum of the transcript FPKMs. You might read one of the original papers describing how this is done: Trapnell et al., Nature Biotechnology volume 28, pages 511–515 (2010). But of course, there are a variety of ways to estimate these values.

ADD COMMENTlink written 3.0 years ago by seidel7.4k
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