Question: DESeq2 for non-model organisms
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2.8 years ago by
####190
####190 wrote:

I want to perform RNA-Seq analysis on non-model organism data using DESeq2 , as its well known that DESeq2 uses Biomart for organism references like : hsapiens or mmusculus for human or mouse My organism is non-model and I am trying to find out option/s to do so.

Any inputs on this...??

Thanks

rna-seq deseq2 • 754 views
ADD COMMENTlink modified 2.8 years ago • written 2.8 years ago by ####190
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gravatar for genomax
2.8 years ago by
genomax75k
United States
genomax75k wrote:

As long as you can generate a matrix of counts (unique genes/ID's as rows, samples as columns), you can use DESeq2 for DE analysis.

ADD COMMENTlink written 2.8 years ago by genomax75k
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2.8 years ago by
####190
####190 wrote:

Cannot generate that.

Was looking for a way to call genome via Biomart as the genome is there in Ensembl but from listDatasets(ensembl) in R cannot see or find that organism.

ADD COMMENTlink modified 2.8 years ago • written 2.8 years ago by ####190

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

What do you mean by "call genome via BioMart"? What package are you referring to in listDatasets command?

If you have aligned bam files you can count reads based on features you are interested in (e.g. exons, genes etc) to generate the count matrix. I use featureCounts to do this before getting to DESeq2. You can use featureCounts as a standalone program or as an R-package if you prefer that.

ADD REPLYlink modified 2.8 years ago • written 2.8 years ago by genomax75k

I hope you can ignore un-organized way of posting...

So I do and I have used featureCounts as well. My point is not generating matrix so my point is to use non-model organism for RNA-seq analysis using DESeq2 and as you know DESeq2 has a BiomaRt r package , which can help user to use particular organism by just mentioning the name of the organism as mentioned in the following link: http://www.ensembl.org/info/data/biomart/biomart_r_package.html in the same link you can see the option listDatasets function of BiomaRt in R which lists out the organism present in biomart R package. I hope it is clear now.

I could only manage to generate the count matrix for the analysis but facing problem in further steps of analysis.

ADD REPLYlink written 2.8 years ago by ####190
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