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bio-read-alignment-hisat2-alignment

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Align RNA-seq reads with HISAT2, a memory-efficient splice-aware aligner. Use when STAR's memory requirements are too high or for general RNA-seq alignment.

When to use

• Align RNA-seq reads with HISAT2
• Build HISAT2 index
• Align paired-end reads
• Align single-end reads
• Handle stranded libraries
• Discover novel splice junctions
• Two-pass alignment
• Prepare BAM for quantification

When not to use

• STAR alignment
• Alignment-free quantification
• Differential expression analysis

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