Question: cuffdiff outpuit interpretation, splicing and promoter differntial expression
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gravatar for nishashoolini.phd
15 months ago by
nishashoolini.phd0 wrote:

dear all i have read many posts but still unable to understand that in cuffdiff output what does promoter differntial expression file explains? i request you to please provide me some input over the same. does it lists no. of genes using common promoter? what does the fpkm value shows..is it for the promoter? similarly the splice junction diff expn file..what does each junction represent?

thanks in advanc e

ADD COMMENTlink modified 15 months ago • written 15 months ago by nishashoolini.phd0
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gravatar for Jennifer Hillman Jackson
15 months ago by
United States
Jennifer Hillman Jackson23k wrote:

Hello,

The dataset/file formats are described here under the sections named like "Differential splicing tests - XXX": http://cole-trapnell-lab.github.io/cufflinks/cuffdiff/

Scientific details are also covered under this RNA-seq tutorial: https://github.com/nekrut/galaxy/wiki/Reference-based-RNA-seq

Promoter differential expression file questions:

  • does it lists no. of genes using common promoter? - Each gene is listed distinctly. Different genes do not share a common promoter site - instead, the transcripts associated with the same promoter will be grouped into the same gene by the tool, the supplied reference annotation, or both (depending on the parameters/inputs)

  • what does the fpkm value shows..is it for the promoter? - FPKM is calculated for four classes of features (promoter is not included independently as it is covered by the gene differential expression test). See the section "Differential expression tests" in the first (manual) link above.

  • similarly the splice junction diff expn file..what does each junction represent? - A splice site present in the input NGS reads used to create transcripts/isoforms, the supplied reference annotation, or both (also depends on the parameters/inputs)

Hopefully this helps! Jen, Galaxy team

ADD COMMENTlink written 15 months ago by Jennifer Hillman Jackson23k
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gravatar for nishashoolini.phd
15 months ago by
nishashoolini.phd0 wrote:

hi thank you jen for your time and reply. i might be bothering you too much but once again different transcripts pooled into same gene on the basis of usage of common promoter lie in each entry of promoter diff exp file?....how does it shows promoter diff expn.? did see the link provided. kindly help thanks

ADD COMMENTlink written 15 months ago by nishashoolini.phd0
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