smallRNA plugin

Use the smallRNA plugin to analyze microRNA (miRNA) reads. Reads are aligned to mature miRNAs using the TMAP or bowtie2 alignment software that is bundled with the plugin. Unmapped reads are further aligned to the whole‑genome to rescue miRbase unaligned reads and count other RNA molecules (tRNAs, rRNAs, mRNAs, and so on). miRNA raw counts are generated using featureCounts software.