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bio-workflows-clip-pipeline

Maintainer FreedomIntelligence · Last updated April 1, 2026

CLIP-seq: peak calling → binding site annotation → motif discovery.

OpenClawNanoClawAnalysisReproductionbio-workflows-clip-pipeline🧠 bioos extended suitebioos extended bioinformatics suiteclip

Original source

FreedomIntelligence/OpenClaw-Medical-Skills

https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-workflows-clip-pipeline

Maintainer: FreedomIntelligence
License: MIT
Last updated: April 1, 2026

Skill Snapshot

Key Details From SKILL.md

2 min

Key Notes

fastqc reads.fastq.gz -o qc_pre/.

Source Doc

Excerpt From SKILL.md

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

eCLIP (10nt UMI at 5' end)

umi_tools extract
--stdin=reads.fastq.gz
--bc-pattern=NNNNNNNNNN
--stdout=extracted.fastq.gz
--log=umi_extract.log

iCLIP (5nt experimental barcode + 5nt UMI)

umi_tools extract
--stdin=reads.fastq.gz
--bc-pattern=NNNNNXXXXX
--stdout=extracted.fastq.gz

Use cases

Use bio-workflows-clip-pipeline for genomics and bioinformatics workflows.
Apply bio-workflows-clip-pipeline to sequencing, variant, or omics analysis tasks.

Not for

Do not rely on this catalog entry alone for installation or maintenance details.

Upstream Related Skills

clip-seq/clip-preprocessing - Detailed preprocessing
clip-seq/clip-alignment - Alignment optimization
clip-seq/clip-peak-calling - Peak caller comparison
clip-seq/binding-site-annotation - Feature annotation
clip-seq/clip-motif-analysis - Motif discovery

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