Purdue University

Commands

• extract_exons.py
• extract_splice_sites.py
• hisat2
• hisat2-align-l
• hisat2-align-s
• hisat2-build
• hisat2-build-l
• hisat2-build-s
• hisat2-inspect
• hisat2-inspect-l
• hisat2-inspect-s
• hisat2_extract_exons.py
• hisat2_extract_snps_haplotypes_UCSC.py
• hisat2_extract_snps_haplotypes_VCF.py
• hisat2_extract_splice_sites.py
• hisat2_read_statistics.py
• hisat2_simulate_reads.py

Module

You can load the modules by:

module load biocontainers
module load hisat2

Example job

Using #!/bin/sh -l as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use #!/bin/bash instead.

To run HISAT2 on our clusters:

#!/bin/bash
#SBATCH -A myallocation     # Allocation name 
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=hisat2
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
ml biocontainers hisat2

hisat2-build genome.fa genome

# for single-end FASTA reads DNA alignment
hisat2 -f -x genome -U reads.fa -S output.sam --no-spliced-alignment

# for paired-end FASTQ reads alignment
hisat2 -x genome -1 reads_1.fq -2 read2_2.fq -S output.sam