having up-regulated and down-regulated isoforms in Trinity output
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
1 answer
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.
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Devon Ryan
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I could not understand your experimental design. What is your control? 2 samples 1 replicate?