Using DESeq2 for DE analysis of microRNA data

Question

[Denis]

I'm trying to do DE analysis on Illumina plant miRNA-Seq data. I'm wondering if DESeq2 is the best choice for that? I'd prefer to stick to DESeq2 as i already used that for mRNA DE study, if it's suitable for miRNA of course. I'm wondering if there is some specifics in doing microRNA DE analysis in comparison to those on mRNA data? Could you advise me please?

Answer 1

[ATpoint]

Nothing wrong with that if you start with the raw counts. I suggest you browse the web for this, especially support.bioconductor.org where the DESeq2 developer has commented on mutliple questions towards DESeq2 + miRNA.

[Denis]

Thank you very much! It will definitely make sense.