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ago-clip-mirna-targets

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Identify direct miRNA-target interactions from AGO HITS-CLIP, AGO-CLEAR-CLIP (chimeric reads), HEAP (Halo-Ago2 mouse), chimeric eCLIP / miR-eCLIP (deep miRNA-target profiling), or CLASH using chimeric-read processing pipelines, seed-pairing analysis, and 3' auxiliary pairing rules. Use when distinguishing direct miRNA targets from indirect, integrating CLIP-derived target maps with TargetScan / miRDB / DIANA predictions, applying canonical 7mer-8mer seed matching with 3' UTR context, or recovering miRNA-mRNA chimeras at scale.

When to use

• Identify direct miRNA-target interactions
• Distinguish direct miRNA targets from indirect
• Integrate CLIP-derived target maps with TargetScan / miRDB / DIANA predictions
• Apply canonical 7mer-8mer seed matching with 3' UTR context
• Recover miRNA-mRNA chimeras at scale
• Process AGO HITS-CLIP, AGO-CLEAR-CLIP, HEAP, chimeric eCLIP / miR-eCLIP, or CLASH data

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