bio-rnaseq-qc
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.
npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-rnaseq-qc --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
## Version Compatibility Reference examples tested with: NCBI BLAST+ 2.15+, numpy 1.26+, picard 3.1+, pysam 0.22+, samtools 1.19+ Before using code patterns, verify installed versions match. If versions differ: - Python: `pip show <package>` then `help(module.function)` to check signatures - CLI: `<tool> --version` then `<tool> --help` to confirm flags If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying. # RNA-seq Quality Control 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` ## rRNA Contamination Detection High rRNA content indicates failed rRNA depletion or polyA selection. ### SortMeRNA (NCBI BLAST+) ```bash sortmerna \ --ref rRNA_databases/smr_v4.3_default_db.fasta \ --reads sample.fastq.gz \ --aligned rRNA_reads \ --other non_rRNA_reads \ --fastx \ --threads 8 rrna_count=$(grep -c "^@" rRNA_reads.fastq 2>/
- Version Compatibility
- rRNA Contamination Detection
- SortMeRNA (NCBI BLAST+)
- BLAST Against rRNA (NCBI BLAST+)
- Expected rRNA Levels
- Strandedness Verification
- RSeQC inferexperiment (NCBI BLAST+)
- Output Interpretation
- Strand Inference
- Salmon Strandedness (NCBI BLAST+)
- Gene Body Coverage
- RSeQC geneBodycoverage (NCBI BLAST+)
- Interpretation
- Read Distribution
sortmerna \
echo "rRNA: ${rrna_pct}%"
seqkit sample -n 10000 sample.fastq.gz | seqkit fq2fa > sample_10k.fasta
blastn -query sample_10k.fasta -db rrna_db -outfmt 6 -evalue 1e-10 -max_target_seqs 1 | wc -l
infer_experiment.py -i aligned.bam -r genes.bed
salmon quant -i index -l A -r sample.fastq.gz -o quant/
grep "library_types" quant/lib_format_counts.json
geneBody_coverage.py \
read_distribution.py -i aligned.bam -r genes.bed > distribution.txt
tin.py -i aligned.bam -r genes.bed > tin_scores.txtWhat does the bio-rnaseq-qc skill do?
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.
How do I install it?
Run `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-rnaseq-qc --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From FreedomIntelligence/OpenClaw-Medical-Skills, a repository with 2,909 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.