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mirge3-analysis

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Quantifies known miRNAs, isomiRs, tRFs, and A-to-I editing fast with miRge3.0 by aligning collapsed reads to curated miRBase or MirGeneDB libraries. Use when choosing miRBase versus MirGeneDB as the reference; deciding whether to collapse isomiRs to the parent miRNA or keep 5'-isomiRs separate (they shift the seed and retarget); confirming the organism is among the six supported species; or remembering that RPM output is for display only and raw counts go to DESeq2/edgeR.

When to use

• Quantifying known miRNAs
• Quantifying isomiRs
• Quantifying tRFs
• Detecting A-to-I editing
• Choosing miRBase versus MirGeneDB reference
• Collapsing isomiRs to parent miRNA
• Keeping 5'-isomiRs separate
• Confirming organism support

When not to use

• Genome-wide de novo discovery
• Unsupported organisms
• Novel miRNA discovery

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