Question: having up-regulated and down-regulated isoforms in Trinity output
gravatar for Whoknows
5.4 years ago by
Whoknows860 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 • 1.5k views
ADD COMMENTlink modified 5.4 years ago by Devon Ryan98k • written 5.4 years ago by Whoknows860

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

ADD REPLYlink written 5.4 years ago by tiago2112871.3k
gravatar for Devon Ryan
5.4 years ago by
Devon Ryan98k
Freiburg, Germany
Devon Ryan98k 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 5.4 years ago by Devon Ryan98k
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1555 users visited in the last hour