Question: denovo transcriptome assembly
0
gravatar for 1234anjalianjali1234
7 days ago by
India
1234anjalianjali123430 wrote:

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 • 169 views
ADD COMMENTlink modified 6 days ago by kristoffer.vittingseerup1.8k • written 7 days ago by 1234anjalianjali123430

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 modified 7 days ago • written 7 days ago by genomax68k

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

ADD REPLYlink modified 7 days ago • written 7 days ago by 1234anjalianjali123430
1

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 written 7 days ago by genomax68k

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

Thankyou

ADD REPLYlink written 7 days ago by 1234anjalianjali123430
0
gravatar for kristoffer.vittingseerup
6 days ago by
European Union
kristoffer.vittingseerup1.8k wrote:

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 written 6 days ago by kristoffer.vittingseerup1.8k
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