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star-alignment

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Aligns RNA-seq reads to a genome with STAR, the fast splice-aware aligner whose splice-junction database (built from a GTF at sjdbOverhang = readlength-1) and two-pass mode set junction sensitivity, whose 255-for-unique MAPQ breaks GATK, and whose GeneCounts output reveals library strandedness. Use when RNA reads must be placed on the genome for novel-isoform discovery, fusion detection, RNA variant calling, coverage tracks, splicing QC, or single-cell (STARsolo). Memory-constrained RNA alignment is hisat2-alignment; DE on known transcripts only should skip alignment for rna-quantification/alignment-free-quant; the QC gate and contig-naming reconciliation are alignment-files; counting is rna-quantification; DNA is bwa-alignment/bowtie2-alignment.

When to use

• RNA splice-aware mapping
• index generation
• two-pass alignment
• GeneCounts output
• chimeric/fusion output
• novel-isoform discovery
• fusion detection
• RNA variant calling

When not to use

• DNA alignment
• long read alignment
• memory-constrained RNA alignment
• DE on known transcripts only
• counting reads over genes/transcripts
• single-cell droplet/plate counting
• QC gate
• contig-naming reconciliation

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