Is it possible to do differential analyis on mirdeep2 outcome?

Question

[gulamaltab]

Mirdeep2 outcome provides total read count and mature read counts, would it be appropriate to use these counts to do differential analysis using Deseq2?

Thanks

[Buffo]

Yes, but I recommend you to use just mature read counts since the total count may include precursor sequences and consequently potential iso-mirs.

[gulamaltab]

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

[sabaghianamir70]

I did quantify my data mirdeep2 quantifier in galaxy. how turn it to the file which can be recognized from deseq2 in galaxy ?