RESEARCH USE
Where HISAT2 fits
Choose a standard or graph index from the reference genome, known splice sites, variants, and study objective, then run splice-aware alignment of RNA-seq reads. When transcript assembly is planned, use the corresponding output option. Preserve reference and annotation releases, index provenance, strandedness, alignment parameters, software version, and quality metrics.
Research tasks
- Align RNA-seq reads to a reference genome
- Build graph indexes with known transcripts or variants
- Generate splice-aware alignments for transcript assembly and expression analysis
What to evaluate before use
- Index type, annotation release, and strandedness settings materially affect splice junctions and counts; defaults are not universally appropriate.
- An alignment is not direct evidence for transcript existence or differential expression. Multimapping, pseudogenes, repeats, and sample quality need downstream treatment.
Verification note
This entry summarizes the resource's role without assessing scientific accuracy or endorsing its outputs. Features and terms can change; consult the official source before adopting it for consequential work.
RNA-seqsplice-aware alignment
Last verified: 2026-09-17
Source: official documentation ↗