Question: #rna-seq 2 tissue, 2 different individual, no replicate, what can i analysis?
0
gravatar for t2g4free
2.4 years ago by
t2g4free0
t2g4free0 wrote:

I am a amateur about bioinfor. So just as the title, what can I analysis? 2 individual(the same species and not the same age) , 2 tissue rna-seq data, no any replicate Thx

rna-seq • 774 views
ADD COMMENTlink modified 2.4 years ago • written 2.4 years ago by t2g4free0

Hi. There is not much you can do if you have no replicates. You can settle with a fold change descriptive analysis, or you can follow one of the steps listed on section 2.11 of the edgeR manual, athough I would take the results from this with a grain of salt.

ADD REPLYlink written 2.4 years ago by biofalconch410

Thx for all reply. Except DE analysis, what else can I do?

ADD REPLYlink written 2.4 years ago by t2g4free0

Please use ADD COMMENT/ADD REPLY when responding to existing posts to keep threads logically organized.

ADD REPLYlink written 2.4 years ago by genomax75k
0
gravatar for Ace
2.4 years ago by
Ace70
Ace70 wrote:

DeSeq (not DeSeq2) can do differential analysis without replicates. You could choose to look at the different tissues, making the assumption your individuals are similar enough to draw some conclusions about the population. This would be a very dirty analysis, but it might make good practice for a beginner who is still learning the pipelines as it could be processed pretty quick.

ADD COMMENTlink written 2.4 years ago by Ace70
1

Supplementary answer in addition to this: https://support.bioconductor.org/p/61531/

ADD REPLYlink modified 2.4 years ago • written 2.4 years ago by genomax75k

Thx for reply, and what else can I do except DE analyis?

ADD REPLYlink written 2.4 years ago by t2g4free0
1

I suppose with any high-enough coverage/quality RNA-seq sample you can look to do transcriptome assembly and isoform discovery but if you're in a model organism that's still not very novel, so again would only be good for practice. Even in bioinformatics work, your time is best spent if you know what kind of analysis you want to do before you get your samples :)

ADD REPLYlink written 2.4 years ago by Ace70
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: 729 users visited in the last hour