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.

Q2: How are miRNA expression values reported by the qunatification module normalized?
A:  Expression values are normalized by library size and multiplied by a factor of 10E6 which corresponds
	technically to counts per million mapped miRNA reads.
    The library size is the total number of reads mapping to miRNA precursors.

Q3: Does miRDeep2 differential miRNA expression profiling?
A:  No, but the output from the quantification module can be used
    directly as input for specialized differential expression
	tools. 
 



