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

bio-splicing-pipeline

Maintainer FreedomIntelligence · Last updated April 1, 2026

Alternative splicing analysis: rMATS → PSI → differential → sashimi.

OpenClawNanoClawAnalysisReproductionbio-splicing-pipeline🧠 bioos extended suitebioos extended bioinformatics suitealternative

Original source

FreedomIntelligence/OpenClaw-Medical-Skills

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

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

Skill Snapshot

Key Details From SKILL.md

2 min

Key Notes

Complete workflow from raw RNA-seq to differential splicing results.
fastp \ -i sample_R1.fastq.gz \ -I sample_R2.fastq.gz \ -o sample_clean_R1.fastq.gz \ -O sample_clean_R2.fastq.gz \ --detect_adapter_for_pe \ --thread 8 \ -h sample_fastp.html.

Source Doc

Excerpt From SKILL.md

First pass to detect novel junctions

STAR
--runThreadN 8
--genomeDir star_index/
--readFilesIn sample_R1.fastq.gz sample_R2.fastq.gz
--readFilesCommand zcat
--outFileNamePrefix sample_pass1_
--outSAMtype BAM Unsorted
--outSJfilterOverhangMin 8 8 8 8
--alignSJDBoverhangMin 1

(Combine SJ.out.tab files from all samples)

cat *_SJ.out.tab > combined_SJ.out.tab

Second pass with combined junctions

STAR
--runThreadN 8
--genomeDir star_index/
--readFilesIn sample_R1.fastq.gz sample_R2.fastq.gz
--readFilesCommand zcat
--sjdbFileChrStartEnd combined_SJ.out.tab
--outFileNamePrefix sample_
--outSAMtype BAM SortedByCoordinate
--outSJfilterOverhangMin 8 8 8 8
--alignSJDBoverhangMin 1
--quantMode GeneCounts