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bulkrna-read-alignment

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Load when summarising STAR / HISAT2 / Salmon alignment-rate logs in bulk RNA-seq. Skip if data is raw FASTQ (use bulkrna-read-qc) or already counted (use bulkrna-qc), or for genome-DNA alignment (use genomics-alignment).

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bulkrna-read-alignment

When to use

Run after the aligner / quantifier finishes, on the log file produced by STAR (Log.final.out), HISAT2 (.log), or Salmon (meta_info.json). Yields a one-page mapping-rate summary, strandedness inference, and a gene-body coverage profile — the QC bridge between raw FASTQ and the count matrix.

Inputs & Outputs

InputFormatRequired
Aligner logLog.final.out (STAR), .log (HISAT2), meta_info.json (Salmon)yes (or --demo)
OutputPathNotes
Mapping summary figurefigures/mapping_summary.pngunique vs multi vs unmapped
Gene body coveragefigures/gene_body_coverage.png5'→3' bias profile
Alignment compositionfigures/alignment_composition.pngbreakdown of mapping outcomes
Stats tabletables/alignment_stats.csvparsed numeric metrics
Reportreport.md + result.jsonalways

Flow

  1. Auto-detect aligner from filename (bulkrna_read_alignment.py:305-311): log.final.out → STAR; meta_info → Salmon; otherwise → HISAT2.
  2. Parse the log into a numeric stats dict.
  3. Run quality assessment heuristics (high/medium/low mapping-rate buckets).
  4. Render figures and write report.md + tables/alignment_stats.csv.

Gotchas

  • Aligner detection is filename-based, not content-based. bulkrna_read_alignment.py:305-311 dispatches by input_path.name.lower() — anything that is neither log.final.out nor meta_info (case-insensitive substring) is silently parsed as a HISAT2 log. A renamed STAR log will produce nonsense. Pass --method star explicitly if your STAR file isn't named conventionally.
  • The skill consumes the LOG, not the BAM. Feeding a .bam or .sam file as --input will not raise — the parser just finds zero matchable lines and reports an empty stats dict. Sanity-check result.json["summary"]["total_reads"] is non-zero before trusting any downstream summary.
  • Gene body coverage is synthetic in --demo mode (bulkrna_read_alignment.py:142-150). The 5'→3' bias profile in demo runs is a fixed reproducible curve, not derived from real input — useful for layout previews but not for assessing real RNA degradation.

Key CLI

python omicsclaw.py run bulkrna-read-alignment --demo
python omicsclaw.py run bulkrna-read-alignment --input Log.final.out --output results/

See also

  • references/parameters.md — every CLI flag and tuning hint
  • references/methodology.md — STAR / HISAT2 / Salmon parsers, strandedness inference
  • references/output_contract.md — exact output directory layout
  • Adjacent skills: bulkrna-read-qc (upstream FASTQ QC), bulkrna-qc (downstream count-matrix QC), genomics-alignment (DNA-alignment sibling: BAM/SAM, not log files)