bio-read-alignment-star-alignment
Align RNA-seq reads with STAR (Spliced Transcripts Alignment to a Reference). Supports two-pass mode for novel splice junction discovery. Use when aligning RNA-seq data requiring splice-aware alignment.
npx skills add BioTender-max/awesome-bio-agent-skills --skill star-alignment --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
## Version Compatibility Reference examples tested with: STAR 2.7.11+, Subread 2.0+, fastp 0.23+, kallisto 0.50+ Before using code patterns, verify installed versions match. If versions differ: - CLI: `<tool> --version` then `<tool> --help` to confirm flags If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying. # STAR RNA-seq Alignment **"Align RNA-seq reads with STAR"** → Map RNA-seq reads to a reference genome with fast, sensitive splice-aware alignment. Preferred for large datasets and downstream fusion/chimeric read detection. - CLI: `STAR --runMode alignReads --genomeDir index/ --readFilesIn R1.fq R2.fq --outSAMtype BAM SortedByCoordinate` ## Generate Genome Index ```bash # Basic index generation STAR --runMode genomeGenerate \ --runThreadN 8 \ --genomeDir star_index/ \ --genomeFastaFiles reference.fa \ --sjdbGTFfile annotation.gtf \ --sjdbOverhang 100 # Read length - 1 ``` ## Index with Specific Read Length ```bash # For 150bp reads, use sjdbOverhang=149 STAR --runMode genomeGenerate \ --runThreadN 8 \ --genomeDir star_index_150/ \ --genomeFastaFiles reference.fa \ --sjdbGT
- Version Compatibility
- Generate Genome Index
- Index with Specific Read Length
- Basic Alignment
- Single-End Alignment
- Two-Pass Mode
- Quantification Mode
- ENCODE Options
- Fusion Detection
- Output Files
- Memory Requirements
- Shared Memory Mode
- Key Parameters
- Related Skills
Basic index generation STAR --runMode genomeGenerate \ For 150bp reads, use sjdbOverhang=149 Paired-end alignment STAR --runThreadN 8 \ Two-pass mode for better novel junction detection Output gene counts (like featureCounts) ENCODE recommended settings For chimeric/fusion detection Reduce memory for limited systems
What does the bio-read-alignment-star-alignment skill do?
Align RNA-seq reads with STAR (Spliced Transcripts Alignment to a Reference). Supports two-pass mode for novel splice junction discovery. Use when aligning RNA-seq data requiring splice-aware alignment.
How do I install it?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill star-alignment --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From BioTender-max/awesome-bio-agent-skills, a repository with 135 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.