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bio-rnaseq-qc

Maintainer FreedomIntelligence · Last updated April 1, 2026

RNA-seq specific quality control including rRNA contamination detection, strandedness verification, gene body coverage, and transcript integrity metrics. Use when validating RNA-seq libraries before differential expression analysis.

OpenClawNanoClawAnalysisReproductionbio-rnaseq-qc🧬 bioinformatics (gptomics bio-* suite)bioinformatics — sequencing & read qcrna

Original source

FreedomIntelligence/OpenClaw-Medical-Skills

https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-rnaseq-qc

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

Skill Snapshot

Key Details From SKILL.md

2 min

Key Notes

CLI: infer_experiment.py, read_distribution.py (RSeQC).
CLI: picard CollectRnaSeqMetrics.
RNA-seq specific QC metrics beyond general read quality.
Check RNA-seq alignment quality" → Assess gene body coverage, read distribution (exonic/intronic/intergenic), strand specificity, and rRNA contamination rate. CLI: infer_experiment.py, read_distribution.py (RSeQC) CLI: picard CollectRnaSeqMetrics.

Source Doc

Excerpt From SKILL.md

rRNA Contamination Detection

High rRNA content indicates failed rRNA depletion or polyA selection.

Expected rRNA Levels

Library Type	Expected rRNA
PolyA selected	< 5%
rRNA depleted	< 10%
Total RNA	50-80%

Strand Inference

Tool Setting	1++,1--,2+-,2-+	1+-,1-+,2++,2--
Forward (dUTP)	~0	~1
Reverse (Illumina)	~1	~0
Unstranded	~0.5	~0.5

Use cases

Use when validating RNA-seq libraries before differential expression analysis.

Not for

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

Upstream Related Skills

quality-reports - General FastQC
fastp-workflow - Read trimming
alignment-files/alignment-validation - General BAM QC
rna-quantification/featurecounts-counting - Quantification after QC

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