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clip-pipeline

separate

End-to-end CLIP-seq pipeline from FASTQ to ENCODE-compliant binding sites, single-nucleotide crosslink maps, annotation, motifs, and (optionally) differential binding. Use when running the full Yeo lab eCLIP / iCLIP / iCLIP2 / iCLIP3 / irCLIP / PAR-CLIP analysis with SMInput control, protocol-specific UMI extraction, ENCODE STAR parameters, CLIPper or Skipper peak calling with stringent log2 FC and -log10 p thresholds, IDR rescue and self-consistency QC, and downstream motif registration with mCross or PEKA.

When to use

• running the full Yeo lab eCLIP / iCLIP / iCLIP2 / iCLIP3 / irCLIP / PAR-CLIP analysis
• protocol-specific UMI extraction
• ENCODE STAR parameters
• CLIPper or Skipper peak calling with stringent log2 FC and -log10 p thresholds
• IDR rescue and self-consistency QC
• downstream motif registration with mCross or PEKA
• single-nucleotide crosslink maps
• differential binding

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