Hello
I have used miRDeep2 to predict novel miRNAs in my small RNA datasets. The program generates a table with several columns like miRDeep2 score, estimated false positive, estimated true positive and etc. Also, there are the lists of both novel and known predicted miRNAs. Actually I can not understand the relation among these parameters, and generally when these parameters are considered as optimal for being a high probable novel miRNA candidate?
Responses would be appreciated in advance.
Hi Zahra,
Most of the parameters are explained in detail in different publications.
Nevertheless, for the identification of novel miRNA candidates authors use different parameters. From what I have read, I would say that you should choose a novel microRNA should have a miRDeep score > 4 (but also some authors use 1 sometimes), not present a match with rfam, should present a significant RNAfold ("yes") and a number of mature reads > 10. I would say those are the parameters you should look at to filter the potentially novel microRNAs. Additionally, other authors have used a requirement for novel microRNAs to be expressed in multiple samples from their experiments.
I hope this information has been helpful!
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