nf-core/clipseq

CLIP sequencing analysis pipeline for QC, pre-mapping, genome mapping, UMI deduplication, and multiple peak-calling options.

clipclip-seqpeak-callingrna-rbp-interactions

This pipeline uses DSL1. It will not work with Nextflow versions after 22.10.6. Learn more.

Launch version 1.0.0 https://github.com/nf-core/clipseq

Version history

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Initial release of nf-core/clipseq, created with the nf-core template.

Pipeline summary

Adapter and quality trimming (Cutadapt)
Pre-mapping to e.g. rRNA and tRNA sequences (Bowtie 2)
Genome mapping (STAR)
UMI-based deduplication (UMI-tools)
Crosslink identification (BEDTools)
Bedgraph coverage track generation (BEDTools)
Peak calling (multiple options):
- iCount
- Paraclu
- PureCLIP
- Piranha
Motif detection (DREME)
Quality control:
- Sequencing quality control (FastQC)
- Library complexity (Preseq)
- Regional distribution (RSeQC)
Overall pipeline run and QC summaries and peak calling comparisons (MultiQC)