Discrepancy in short reads counts detection using whole genome (<i>wg-set</i>) and miRNA precursor set (<i>mir-set</i>) as reference. CorderoFrancesca BeccutiMarco ArigoniMaddalena DonatelliSusanna A. CalogeroRaffaele 2012 <p>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 <i>mir-set</i> (4 miRNAs). Red and black dots refer respectively to miRNAs detected in experiment A and B without significant variation between <i>mir-set</i> and <i>wg-set</i>. Green and blue dots refer respectively to miRNAs detected in experiment A and B with significant variation between <i>mir-set</i> and <i>wg-set</i>.</p>