Biostar Beta. Not for public use.
denovo transcriptome assembly
0
Entering edit mode
14 months ago
India

hellow all,

I want to check the differences between two physiologically distinct roots in a plant (do not have reference genome). I have done RNA sequencing using novaseq, and want to do differential gene expression analysis, but i am confused in denovo transcriptome assembly. Do I need to have single assembly using both the samples or two different assemblies respectively and then do the mapping part to find DEG.

Thank you

RNA-Seq Assembly • 250 views
ADD COMMENTlink
0
Entering edit mode

two physiologically distinct roots in a plant

What does that exactly mean? Is it still the same plant species? Are they two samples from two parts of plant roots?

ADD REPLYlink
0
Entering edit mode

Same plant species producing two physiologically distinct roots. Two samples from two different plants of same species.

ADD REPLYlink
1
Entering edit mode

Combining the two samples during de novo assembly should give you additional coverage/a more comprehensive representation.

You keep referring to both samples so is this an n=1 situation for both samples?

ADD REPLYlink
0
Entering edit mode

two kind of samples with triplicates so its n=3.

Thankyou

ADD REPLYlink
0
Entering edit mode
21 months ago
European Union

The best approach is to generate a combined transcriptome from all your samples. You can read more about it, along with some suggestion for bioinformatic tools here.

ADD COMMENTlink

Login before adding your answer.

Similar Posts
Loading Similar Posts
Powered by the version 2.3