Question: having up-regulated and down-regulated isoforms in Trinity output
gravatar for Whoknows
3.9 years ago by
Whoknows740 wrote:

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-regauted and 2 down-regulated isoforms.

How can i discuss it?

Is there any problem with my analysis process?


assembly rna-seq trinity latest • 1.2k views
ADD COMMENTlink modified 3.9 years ago by Devon Ryan91k • written 3.9 years ago by Whoknows740

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

ADD REPLYlink written 3.9 years ago by tiago2112871.1k
gravatar for Devon Ryan
3.9 years ago by
Devon Ryan91k
Freiburg, Germany
Devon Ryan91k wrote:

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.

ADD COMMENTlink written 3.9 years ago by Devon Ryan91k
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