Salmon

Introduction

Salmon is a tool for quantifying the expression of transcripts using RNA-seq data.

For more information, please check:

BioContainers: https://biocontainers.pro/tools/salmon

Home page: https://combine-lab.github.io/salmon/

Versions

• 1.10.1

• 1.9.0

Commands

• salmon

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 salmon 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=salmon
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

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

salmon index -t  Homo_sapiens.GRCh38.cds.all.fa -i salmon_index
salmon quant -i salmon_index -l A -p 24 -1 SRR16956239_1.fastq -2 SRR16956239_2.fastq --validateMappings -o transcripts_quan