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binding-site-annotation

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Annotate CLIP-seq peaks or crosslink sites to RNA features (5'UTR, CDS, 3'UTR, intron, splice junction, snoRNA, tRNA, ncRNA, repeat elements) with ChIPseeker, RCAS, RBP-Maps (Yeo splicing regulatory maps), and bedtools, applying feature-priority hierarchies, transcript-context resolution, and metagene aggregation. Use when characterizing where in transcripts an RBP binds, comparing peak distribution across regions, generating splicing-regulatory maps relative to alternative-splicing events, or distinguishing exonic vs intronic vs UTR binding.

When to use

• Annotate CLIP-seq peaks to RNA features
• Map crosslink sites to 5'UTR, CDS, 3'UTR, intron, splice junction
• Characterize where in transcripts an RBP binds
• Compare peak distribution across regions
• Generate splicing-regulatory maps relative to alternative-splicing events
• Distinguish exonic vs intronic vs UTR binding
• Flag repeat-element overlap
• Generate metagene distributions

When not to use

• ChIP-seq promoter analysis
• Global region distribution without RNA-specific context

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