#!/bin/bash
#SBATCH --time=20:00:00
#SBATCH --nodes=1
#SBATCH --ntasks=40
#SBATCH --ntasks-per-node=40

#generate genome indices using STAR
STAR --runThreadN 6 \
--runMode genomeGenerate \
--genomeDir /scratch/cmp1g20/ref_genome/hg38_index \
--genomeFastaFiles /scratch/cmp1g20/ref_genome/hg38.fa \
--sjdbGTFfile /scratch/cmp1g20/ref_genome/hg38.refGene.gtf \
--sjdbOverhang 99
