STAR RNA-seq Alignment

Generate Genome Index

# Basic index generation
STAR --runMode genomeGenerate \
    --runThreadN 8 \
    --genomeDir star_index/ \
    --genomeFastaFiles reference.fa \
    --sjdbGTFfile annotation.gtf \
    --sjdbOverhang 100    # Read length - 1

Index with Specific Read Length