By 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
.gzperbulkrna_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.
.gzdetection is filename-suffix only (bulkrna_read_qc.py:70checks.endswith(".gz")). A gzipped file misnamed without.gzwill 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)