Recovery of known miRNA, and fraction of known miRNA in the data. (a): Recovery of known miRNAs with different matching criteria and abundance requirements. MiRNA fractions are given with respect to the total number of miRNA loci observed in the data. Abundance levels are minimum expression threshold for a locus. (b): Fraction of known miRNA to total number of loci in the data, at different match criteria and (minimum) abundance levels. Perfect, unique: Allow only reads that match the genome perfectly, and in one place only. Imperfect: Also allow reads that match imperfectly (down to 90% identity), but still in only one position. Multiple mapping: Allow only reads that match perfectly, but up to five places in the genome. All: Allow both perfect and imperfect matching, and mapping up to five places.