HISAT2 RNA-seq Alignment

Build Index

# Basic index (no annotation)
hisat2-build -p 8 reference.fa hisat2_index

# Index with splice sites and exons (recommended)
hisat2_extract_splice_sites.py annotation.gtf > splice_sites.txt
hisat2_extract_exons.py annotation.gtf > exons.txt

hisat2-build -p 8 \
    --ss splice_sites.txt \
    --exon exons.txt \
    reference.fa hisat2_index

Basic Alignment