having up-regulated and down-regulated isoforms in Trinity output

Question

[Whoknows]

Hi friends

I analyzed 2 sample (1 replicate) via Trinity, then I used EdgeR for DEG. (based on "De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis")

Now I have a problem, some of genes have for example 1 up-regulated and 2 down-regulated isoforms.

How can I discuss it?

Is there any problem with my analysis process?

Thanks

[tiago211287]

I could not understand your experimental design. What is your control? 2 samples 1 replicate?

Answer 1

[Devon Ryan]

You're not a biologist, I take it. Changes in relative isoform level are common and not indicative of any sort of problem. What that actually means on a biological level is often completely unknown, however.