Kallisto

Introduction

Kallisto is a program for quantifying abundances of transcripts from bulk and single-cell RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads.

For more information, please check:
BioContainers: https://biocontainers.pro/tools/kallisto
Home page: https://pachterlab.github.io/kallisto/

Versions

0.46.2
0.48.0

Commands

kallisto

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 clusters:

#!/bin/bash
#SBATCH -p PartitionName  # batch, gpu, preempt, mpi or your group's own partition
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH -c 4
#SBATCH --mem=8G
#SBATCH --job-name=kallisto
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module purge
module load kallisto/XXXX ### you can run *module avail kallisto* to check all available versions

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