What does the part "mature miRBase miRNAs not detected by miRDeep2" actually mean in a miRDeep2 analysis? Should those hits be included in results?

Question

[Debasish]

After completion of a miRDeep2 analysis, the results are generated in three different parts, viz., 1) novel miRNAs predicted by miRDeep2, 2) mature miRBase miRNAs detected by miRDeep2 3) mature miRBase miRNAs not detected by miRDeep2. What does this 3rd category actually mean? If these miRNAs are not detected in the analysis then why are those even included in the output? Or does it refer to those miRNAs which have hits in the sample file, but do not have any consensus precursors in their flanking region in the genome? Should I include those hits as identified miRNAs in the final results?

Answer 1

[binaryCode]

From the FAQ: https://github.com/rajewsky-lab/mirdeep2/blob/master/FAQ.md

Q1 What are mature miRBase miRNAs not detected by miRDeep2 in the result files?

A Those miRNAs have not been detected by miRDeep2 due to unusual precursor structures. The miRDeep2 module does de novo miRNA prediction and miRNA precursors or mature sequences that do not fit the assumed biogenesis model were not reported as such. The assignment of being a known miRNA happens in the very end by simple sequence comparison with all predicted miRNA precursors. However, running the quantification module reports expression values for all known miRNAs in your data and thus they will still appear in the miRDeep2 output files in this special category.