Is it possible to do differential analyis on mirdeep2 outcome?
Mirdeep2 outcome provides total read count and mature read counts, would it be appropriate to use these counts to do differential analysis using Deseq2?
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Yes, but I recommend you to use just mature read counts since the total count may include precursor sequences and consequently potential iso-mirs.
Hi thank you very much for the reply. Just to clarify, I can just take the mature read counts from the results.csv and use it for deseq2? Don’t I need to use quantifier? Thanks again
I did quantify my data mirdeep2 quantifier in galaxy. how turn it to the file which can be recognized from deseq2 in galaxy ?