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Data & ReproBioinformatics & GenomicsFreedomIntelligence/OpenClaw-Medical-SkillsData & Reproduction
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bio-splicing-quantification

Maintainer FreedomIntelligence · Last updated April 1, 2026

Quantifies alternative splicing events (PSI/percent spliced in) from RNA-seq using SUPPA2 from transcript TPM or rMATS-turbo from BAM files. Calculates inclusion levels for skipped exons, alternative splice sites, mutually exclusive exons, and retained introns. Use when measuring splice site usage or isoform ratios from RNA-seq data.

OpenClawNanoClawAnalysisReproductionbio-splicing-quantification🧬 bioinformatics (gptomics bio-* suite)bioinformatics — sequencing & read qcquantifies

Original source

FreedomIntelligence/OpenClaw-Medical-Skills

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

Maintainer
FreedomIntelligence
License
MIT
Last updated
April 1, 2026

Skill Snapshot

Key Details From SKILL.md

2 min

Key Notes

  • Quantify alternative splicing events as PSI (percent spliced in) values from RNA-seq data.
  • subprocess.run([ 'suppa.py', 'generateEvents', '-i', gtf_file, '-o', output_prefix, '-f', 'ioe', # IOE format for PSI calculation '-e', 'SE', 'SS', 'MX', 'RI', 'FL' # All event types ], check=True).

Source Doc

Excerpt From SKILL.md

Event Types

TypeCodeDescription
Skipped exonSEExon inclusion/exclusion
Alternative 5' splice siteA5SSAlternative donor site
Alternative 3' splice siteA3SSAlternative acceptor site
Mutually exclusive exonsMXEOne of two exons included
Retained intronRIIntron retention

SUPPA2 (transcript TPM-based)

  • Input: Transcript TPM from Salmon/kallisto
  • Faster, requires transcript quantification
  • Better for isoform-level analysis

rMATS-turbo (BAM-based)

  • Input: Aligned BAM files
  • Junction read counting
  • Better for novel junction discovery

Use cases

  • Use when measuring splice site usage or isoform ratios from RNA-seq data.

Not for

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

Upstream Related Skills

  • differential-splicing - Compare PSI between conditions
  • rna-quantification/alignment-free-quant - Generate transcript TPM for SUPPA2
  • read-alignment/star-alignment - Align reads with junction detection

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