Discovers novel miRNAs and quantifies known miRNAs with miRDeep2 by scoring genome-mapped read stacks against the Dicer/Drosha biogenesis signature. Use when deciding whether a study needs de novo discovery at all versus known-miRNA quantification; choosing the species and related-species miRBase references; reading the miRDeep2 score as a signal-to-noise hypothesis rather than a fixed cutoff; or filtering novel candidates against tRNA/rRNA loci to reject the classic false positives.
