bulkrna-read-alignment

name	bulkrna-read-alignment
description	RNA-seq read alignment and quantification statistics — STAR/HISAT2/Salmon log parsing, mapping rate, unique/multi-mapped reads, library strandedness, gene body coverage.
version	0.3.0
author	OmicsClaw
license	MIT
tags	["bulkrna","alignment","STAR","HISAT2","Salmon","mapping-rate","strandedness"]
requires	["numpy","pandas","matplotlib"]
metadata	{"omicsclaw":{"domain":"bulkrna","emoji":"🧬","trigger_keywords":["RNA-seq alignment","STAR","HISAT2","Salmon","mapping rate","read alignment","alignment QC"],"allowed_extra_flags":["--method","--species"],"legacy_aliases":["bulk-align-reads"],"saves_h5ad":false}}

Bulk RNA-seq Read Alignment & Quantification Statistics

Parses alignment logs from STAR, HISAT2, or Salmon to produce comprehensive mapping quality metrics. When run in demo mode, generates synthetic alignment statistics to demonstrate the full reporting pipeline.

Core Capabilities

• Parse STAR Log.final.out, HISAT2 summary, or Salmon meta_info.json
• Compute total reads, uniquely mapped, multi-mapped, unmapped rates
• Alignment quality assessment (unmapped > 20% = warning, > 40% = fail)
• Strandedness estimation from alignment stats
• Library complexity estimation
• Gene body coverage distribution (5' to 3')

Why This Exists

• Without it: Users manually inspect STAR/HISAT2/Salmon logs, compute mapping rates in spreadsheets, and lack standardized quality thresholds.
• With it: A single command parses any common RNA-seq aligner output and produces publication-ready figures with automatic quality assessment.
• Why OmicsClaw: Bridges the gap between raw FASTQ QC and count matrix QC, completing the upstream portion of the bulk RNA-seq pipeline.

Input Formats

Format	Extension	Description
STAR log	Log.final.out	STAR alignment final summary
HISAT2 log	.log	HISAT2 alignment summary
Salmon log	meta_info.json	Salmon quantification metadata

CLI Reference

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

Output Structure

output_directory/
├── report.md
├── result.json
├── figures/
│   ├── mapping_summary.png
│   ├── gene_body_coverage.png
│   └── alignment_composition.png
├── tables/
│   └── alignment_stats.csv
└── reproducibility/
    └── commands.sh

Related Skills

• bulkrna-read-qc — Upstream: FASTQ QC before alignment
• bulkrna-qc — Downstream: count matrix QC after quantification