Data & ReproBioinformatics & GenomicsFreedomIntelligence/OpenClaw-Medical-SkillsData & Reproduction

bio-clip-seq-clip-preprocessing

Maintainer FreedomIntelligence · Last updated April 1, 2026

Preprocess CLIP-seq/eCLIP data: adapter trimming, demultiplexing.

OpenClawNanoClawAnalysisReproductionbio-clip-seq-clip-preprocessing🧠 bioos extended suitebioos extended bioinformatics suitepreprocess

Original source

FreedomIntelligence/OpenClaw-Medical-Skills

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

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

Skill Snapshot

Key Details From SKILL.md

2 min

Key Notes

umi_tools extract \ --stdin=reads_R1.fastq.gz \ --read2-in=reads_R2.fastq.gz \ --bc-pattern=NNNNNNNNNN \ --stdout=R1_umi.fastq.gz \ --read2-out=R2_umi.fastq.gz.
cutadapt \ -a AGATCGGAAGAGCACACGTCT \ -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT \ -m 18 \ -o trimmed_R1.fastq.gz \ -p trimmed_R2.fastq.gz \ R1_umi.fastq.gz R2_umi.fastq.gz.

Source Doc

Excerpt From SKILL.md

First pass: trim 3' adapter

cutadapt -a AGATCGGAAGAGC -m 18 -o pass1.fq.gz input.fq.gz

Second pass: trim 5' adapter (read-through)

cutadapt -g AGATCGGAAGAGC -m 18 -o pass2.fq.gz pass1.fq.gz


## After alignment, deduplicate using UMIs

umi_tools dedup \
    --stdin=aligned.bam \
    --stdout=deduped.bam \
    --paired \
    --method=unique

Use cases

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