star-rna-seq-aligner

npx skills add BioTender-max/awesome-bio-agent-skills --skill star-rna-seq-aligner --agent claude-code

Same command for any agent — swap --agent for codex, cursor, copilot.

# STAR — Spliced RNA-seq Aligner ## Overview STAR (Spliced Transcripts Alignment to a Reference) aligns RNA-seq reads to a genome in a splice-aware manner, identifying novel and annotated splice junctions in a single pass. It generates coordinate-sorted BAM files compatible with samtools, IGV, deeptools, and GATK. STAR's 2-pass mode re-aligns reads using junctions discovered in the first pass, improving sensitivity for novel splice sites. With `--quantMode GeneCounts`, STAR simultaneously produces gene-level read count tables without requiring a separate featureCounts or HTSeq step. ## When to Use - Aligning bulk RNA-seq reads to a reference genome when downstream tools require a BAM file (variant calling, visualization, deeptools) - Running ENCODE-compliant RNA-seq pipelines that mandate genome alignment - Discovering novel splice junctions and alternative splicing events in the dataset - Generating gene count tables alongside BAM alignment in a single step with `--quantMode GeneCounts` - Processing long reads or reads with high mismatch rates by tuning `--outFilterMismatchNmax` - Use **Salmon** instead when you only need transcript/gene quantification and do not need a BAM file —

Install with conda (recommended)
conda install -c bioconda star
Verify
STAR --version
STAR_2.7.11a
Or compile from source
git clone https://github.com/alexdobin/STAR
cd STAR/source && make STAR
STAR --runMode genomeGenerate \
STAR --runThreadN 8 \