Discrepancy in short reads counts detection using whole genome (wg-set) and miRNA precursor set (mir-set) as reference.

We expect that, if reference is not playing any specific role in the alignment procedure, then the same number of counts should be detected independently from the reference set in use. A higher number of miRNAs are shown to be underestimated when the wg-set is used as reference for the mapping (36 miRNAs) with respect to the mir-set (4 miRNAs). Red and black dots refer respectively to miRNAs detected in experiment A and B without significant variation between mir-set and wg-set. Green and blue dots refer respectively to miRNAs detected in experiment A and B with significant variation between mir-set and wg-set.