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bio-read-alignment-star-alignment

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Align RNA-seq reads with STAR (Spliced Transcripts Alignment to a Reference). Supports two-pass mode for novel splice junction discovery.

When to use

• Aligning RNA-seq data requiring splice-aware alignment
• Generating genome index
• Paired-end alignment
• Single-end alignment
• Two-pass mode for novel junction detection
• Quantification mode for gene counts
• Fusion detection
• ENCODE recommended settings

When not to use

• Alignment-free quantification
• Differential expression analysis
• Read preprocessing

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