Software: Kallisto
Description
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.
Available Versions
| Unspecified: | 0.46.2 0.48.0 |
|---|
Detailed usage can be found here: https://github.com/pachterlab/kallisto
Commands
- kallisto
Module
You can load the modules by:
module load biocontainers
module load kallisto/0.48.0
Example job
Using
#!/bin/sh -las shebang in the slurm job script will cause the failure of some biocontainer modules. Please use#!/bin/bashinstead.
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