CLIP-seq Workflow

A Nextflow workflow for end-to-end processing of CLIP-seq data, supporting multiple CLIP protocols.

Overview

Starting from raw FASTQ files (or un-demultiplexed iCLIP data), the workflow processes reads through quality control, adapter trimming, rRNA removal, genome alignment, and UMI deduplication, then runs shoji to extract crosslink sites and produce per-sample and combined count matrices ready for differential binding analysis (see ...