| name | bulkrna-read-qc |
| description | FASTQ quality assessment for bulk RNA-seq — Phred scores, GC content, adapter detection, read length distribution, Q20/Q30 rates. |
| version | 0.3.0 |
| author | OmicsClaw |
| license | MIT |
| tags | ["bulkrna","FASTQ","QC","Phred","GC-content","adapter","read-quality"] |
| requires | ["numpy","pandas","matplotlib"] |
| metadata | {"omicsclaw":{"domain":"bulkrna","emoji":"🔍","trigger_keywords":["FASTQ QC","read quality","Phred","FastQC","adapter","GC content","Q20","Q30"],"allowed_extra_flags":[],"legacy_aliases":["bulk-fastqc"],"saves_h5ad":false}} |
Bulk RNA-seq FASTQ Quality Assessment
Quality assessment of raw FASTQ files for bulk RNA-seq experiments. Computes per-base quality scores, GC content, adapter contamination, read length distribution, and Q20/Q30 rates — a Python implementation of core FastQC metrics.
Core Capabilities
- Per-base Phred quality score profiles
- Q20/Q30 pass rates per sample
- GC content distribution and N content detection
- Adapter sequence contamination check (Illumina TruSeq, Nextera, etc.)
- Read length distribution
- Sequence duplication estimation
Why This Exists
- Without it: Users must install FastQC (Java), run it per file, then use MultiQC to aggregate — a multi-tool, multi-step workflow.
- With it: A single Python command performs core FASTQ QC, generates publication-ready figures, and integrates into the OmicsClaw reporting pipeline.
- Why OmicsClaw: Provides FASTQ-level QC prior to alignment, completing the full bulk RNA-seq pipeline (FASTQ QC → alignment → count matrix QC → ...).
Input Formats
| Format | Extension | Description |
|---|
| FASTQ | .fastq, .fq, .fastq.gz | Raw sequencing reads |
CLI Reference
python omicsclaw.py run bulkrna-read-qc --demo
python omicsclaw.py run bulkrna-read-qc --input reads.fastq.gz --output results/
Output Structure
output_directory/
├── report.md
├── result.json
├── figures/
│ ├── per_base_quality.png
│ ├── gc_content.png
│ ├── read_length_distribution.png
│ └── quality_score_distribution.png
├── tables/
│ └── qc_summary.csv
└── reproducibility/
└── commands.sh
Related Skills
bulkrna-read-alignment — Downstream: alignment after QCbulkrna-qc — Downstream: count matrix QC after quantification
