hisat2.rst

HISAT2

Introduction ~~~~~~~~ HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads (both DNA and RNA) to a population of human genomes as well as to a single reference genome.

For more information, please check its website: https://biocontainers.pro/tools/hisat2 and its home page on Github.

Versions

• 2.2.1

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 ~~~~~ .. warning:: 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