hisat2_run.sh

#!/bin/bash
#SBATCH --job-name=hisat2_run
#SBATCH --mail-user=
#SBATCH --mail-type=ALL
#SBATCH -n 1
#SBATCH -N 1
#SBATCH -c 16
#SBATCH --mem=120G
#SBATCH -o hisat2_run_%j.out
#SBATCH -e hisat2_run_%j.err
#SBATCH --partition=general

export TMPDIR=/home/CAM/$USER/tmp/

module load hisat2

hisat2 -p 16 --dta -x /isg/shared/databases/alignerIndex/plant/Arabidopsis/thaliana/Athaliana_HISAT2/thaliana -q trimmed_SRR3498212.fastq -S athaliana_root_1.sam

hisat2 -p 16 --dta -x /isg/shared/databases/alignerIndex/plant/Arabidopsis/thaliana/Athaliana_HISAT2/thaliana -q trimmed_SRR3498213.fastq -S athaliana_root_2.sam

hisat2 -p 16 --dta -x /isg/shared/databases/alignerIndex/plant/Arabidopsis/thaliana/Athaliana_HISAT2/thaliana -q trimmed_SRR3498215.fastq -S athaliana_shoot_1.sam

hisat2 -p 16 --dta -x /isg/shared/databases/alignerIndex/plant/Arabidopsis/thaliana/Athaliana_HISAT2/thaliana -q trimmed_SRR3498216.fastq -S athaliana_shoot_2.sam