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crosslink-site-detection

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Detect single-nucleotide crosslink (CL) sites in CLIP-seq data using truncation patterns (iCLIP/eCLIP CITS), crosslink-induced mutations (HITS-CLIP CIMS deletions, PAR-CLIP T-to-C), or HMM/kernel-density methods (PureCLIP, PARalyzer, CTK). Use when single-nucleotide resolution is required for motif registration (mCross), allele-specific binding (BEAPR), variant-effect prediction, or comparing crosslink chemistry across CLIP variants.

When to use

• Detect single-nucleotide crosslink sites
• Identify truncation patterns in iCLIP/eCLIP
• Detect crosslink-induced mutations in HITS-CLIP
• Detect T-to-C transitions in PAR-CLIP
• Use HMM or kernel-density methods for CL site detection
• Support motif registration with mCross
• Support allele-specific binding analysis
• Compare crosslink chemistry across CLIP variants

When not to use

• Broad peak calls
• Replacing broad peak calls with single-nt sites

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