# Generating genome indexes for the the STAR+WASP benchmarking runs
STAR --runThreadN 32 --runMode genomeGenerate --genomeDir /home/asiimwe/projects/run_env/alpha_star_wasp_benchmarking/genome_directory --genomeFastaFiles /home/asiimwe/projects/star_wasp/fasta_and_gtf/GRCh38.primary_assembly.genome.fa --sjdbGTFfile /home/asiimwe/projects/star_wasp/fasta_and_gtf/gencode.v39.primary_assembly.annotation.gtf --sjdbOverhang 100