Tools to predict microRNAs in Ascomycota(Fungus)

Question

[MAPK]

I have sequenced data from a few species of Ascomycota. I have degradome sequencing, smallRNA sequencing and whole transcriptome sequencing data from these species of Ascomycota. I want to predict microRNA in these species, and was wondering if there is any tool or method I can follow to predict miRNA using the datasets I have. I have already tried Cleaveland4, but wanted to try other tools as well. Any suggestion?

[ATpoint]

Hi MAPK, given that you already received help for your question from a user, it is not appropriate nor necessary to delete your post. Therefore, I re-opened it.

Answer 1

[Buffo]

mirDeep works fine, but do not use it until you have read and understand the manual and protocol to predict new miRNAs. Small RNAs are not miRNAs by default.