Kallisto

Introduction

Kallisto is a program for quantifying abundances of transcripts from RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads. It is based on the novel idea of pseudoalignment for rapidly determining the compatibility of reads with targets, without the need for alignment.

Detailed usage can be found here: https://github.com/pachterlab/kallisto

Versions

• 0.46.2

• 0.48.0

Commands

• kallisto

Module

You can load the modules by:

module load biocontainers
module load kallisto/0.48.0

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 kallisto on our our clusters:

#!/bin/bash
#SBATCH -A myallocation     # Allocation name
#SBATCH -t 10:00:00
#SBATCH -N 1
#SBATCH -n 24
#SBATCH --job-name=kallisto
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
ml biocontainers kallisto/0.48.0

kallisto index -i transcripts.idx Homo_sapiens.GRCh38.cds.all.fa.gz
kallisto quant -t 24 -i transcripts.idx -o output -b 100  SRR11614709_1.fastq  SRR11614709_2.fastq