kallisto
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
Link to section 'Versions' of 'kallisto' Versions
- 0.46.2
- 0.48.0
Link to section 'Commands' of 'kallisto' Commands
- kallisto
Link to section 'Module' of 'kallisto' Module
You can load the modules by:
module load biocontainers
module load kallisto/0.48.0
Link to section 'Example job' of 'kallisto' 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 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