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Tools to predict microRNAs in Ascomycota(Fungus)

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?

smallrna rna-seq microrna
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updated by Buffo Buffo • written by MAPK MAPK

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.

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written by ATpoint ATpoint

1 answer

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.

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written by Buffo Buffo

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