bio-workflows-clip-pipeline
Installation
SKILL.md
CLIP-seq Pipeline
Pipeline Overview
FASTQ → QC → UMI extract → Trim adapters → Align → Filter → Dedup → Peak call → Annotate → Motifs
CLIP Method Variants
| Method | UMI | Crosslink Site | Adapter |
|---|---|---|---|
| HITS-CLIP | Optional | Deletions | 3' adapter |
| PAR-CLIP | Optional | T→C mutations | 3' adapter |
| iCLIP | Required | 5' of read | 3' adapter |
| eCLIP | Required | 5' of read | 3' adapter |