| name | bulkrna-read-qc |
| description | Load when checking raw FASTQ quality (Phred / GC / adapter / Q20-Q30) before alignment in bulk RNA-seq. Skip if reads are already aligned (use bulkrna-read-alignment) or counted (use bulkrna-qc), or for single-cell FASTQ (use sc-fastq-qc). |
| version | 0.3.0 |
| author | OmicsClaw |
| license | MIT |
| tags | ["bulkrna","FASTQ","QC","Phred","GC-content","adapter","read-quality"] |
| requires | ["numpy","pandas","matplotlib"] |
bulkrna-read-qc
When to use
Run as the first step on raw bulk RNA-seq FASTQ files (single or paired-end)
before aligning. Reports per-base Phred quality, GC content, adapter
contamination signals, read length distribution, and Q20/Q30 fractions —
the metrics needed to decide whether trimming is worth the trouble.
Inputs & Outputs
| Input | Format | Required |
|---|
| FASTQ file | .fastq or .fastq.gz | yes (or --demo) |
| Output | Path | Notes |
|---|
| QC report | report.md + result.json | always |
| Per-base quality | figures/per_base_quality.png | Phred profile across read positions |
| GC distribution | figures/gc_content.png | per-read GC% histogram |
| Length distribution | figures/read_length_dist.png | for variable-length / trimmed input |
Flow
- Open the FASTQ (auto-decompresses
.gz per bulkrna_read_qc.py:70).
- Sample reads, decode Phred quality from header line 4 of each record.
- Compute per-base quality, GC content, length distribution, adapter motif counts.
- Render figures and write
report.md + result.json.
Gotchas
- This is a pure-Python reimplementation of FastQC core metrics, not FastQC itself. Coverage of the more obscure FastQC modules (overrepresented sequences, k-mer enrichment, per-tile quality) is intentionally omitted to keep the skill dependency-free. For full FastQC parity, run FastQC directly and feed the report into MultiQC.
- Phred encoding is assumed to be Phred+33 (Sanger / Illumina 1.8+). Older Illumina 1.3–1.7 platforms used Phred+64 — the per-base quality values will look ~31 points too high if such input is fed in unchanged. Confirm the source platform before trusting Q20/Q30 numbers.
.gz detection is filename-suffix only (bulkrna_read_qc.py:70 checks .endswith(".gz")). A gzipped file misnamed without .gz will be opened as text and silently produce garbage; rename or symlink before running.
Key CLI
python omicsclaw.py run bulkrna-read-qc --demo
python omicsclaw.py run bulkrna-read-qc --input reads.fastq.gz --output results/
See also
references/parameters.md — every CLI flag and tuning hintreferences/methodology.md — Phred decoding, sampling strategy, adapter detectionreferences/output_contract.md — exact output directory layout- Adjacent skills:
bulkrna-read-alignment (downstream after alignment), bulkrna-qc (downstream after counting), sc-fastq-qc (single-cell sibling), genomics-qc (genomic-DNA sibling)
