#rna-seq 2 tissue, 2 different individual, no replicate, what can i analysis?

Question

[t2g4free]

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

[biofalconch]

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.

[GenoMax]

See: best workflow for RNA data analysis without replications and Advice on RNASeq analysis without biological replicates for differential gene expression.

[t2g4free]

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

[GenoMax]

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

Answer 1

[Ace]

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.

[GenoMax]

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

[t2g4free]

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

[Ace]

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 :)