cummeRbund grouping by TSS / CDS / Isoforms

Question

[corend]

I am working on RNA-seq data with cufflinks. I now use cummeRbund to analyze my results.

cummeRbund performs expression quantification between genes / isoforms / CDS or TSS. I understand the difference between gene and isoform expression quantification, but I don't get the difference between TSS, CDS and isoform.

What does it mean to have a gene with differentially expressed isoforms but no DE CDS ? I think I don't get what do they mean when they group by TSS or CDS.

So what does it mean to have DE TSS / CDS / isoforms ? What's the difference between them ?

I couldn't find anything clear enough for me in the cummeRbund vignettes or manual.

I hope I am clear enough,

Thank you,

C

Answer 1

[Kristoffer Vitting-Seerup]

Grouping by TSS means Cuffdiff only considers isoform which shares a TSS and looks for differential usage between those (aka looking for differences in alternative splicing and alternative termination).

Im not completely sure what the test of CDS does - but to me the only thing that makes sense is to compare the different annotated CDS in a gene..:?