Question: denovo transcriptome assembly
0
gravatar for 1234anjalianjali1234
11 months 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 • 448 views
ADD COMMENTlink modified 11 months ago by colindaven2.2k • written 11 months 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 11 months ago • written 11 months ago by genomax83k

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

ADD REPLYlink modified 11 months ago • written 11 months 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 11 months ago by genomax83k

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

Thankyou

ADD REPLYlink written 11 months ago by 1234anjalianjali123430
2
gravatar for kristoffer.vittingseerup
11 months ago by
European Union
kristoffer.vittingseerup3.2k 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 11 months ago by kristoffer.vittingseerup3.2k
1
gravatar for colindaven
11 months ago by
colindaven2.2k
Hannover Medical School
colindaven2.2k wrote:

I haven't tried it, but this program might be helpful. https://genomebiology.biomedcentral.com/articles/10.1186/s13059-017-1284-1

Generally, I'd use Trinity to assemble all transcripts de novo (combined), then try to map each replicate read set to the assembly.

Interproscan is quite good at assessing functionality using ORFs etc from Transdecoder.

ADD COMMENTlink modified 10 months ago • written 11 months ago by colindaven2.2k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1577 users visited in the last hour