Salmon

Introduction

Salmon is a wicked-fast program to produce a highly-accurate, transcript-level quantification estimates from RNA-seq data.

Detailed usage can be found here: https://github.com/COMBINE-lab/salmon

Versions

• 1.10.1

• 1.5.2

• 1.6.0

• 1.7.0

• 1.8.0

• 1.9.0

Commands

• salmon index

• salmon quant

• salmon alevin

• salmon swim

• salmon quantmerge

Module

You can load the modules by:

module load biocontainers
module load 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 our clusters:

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

module --force purge
ml biocontainers salmon

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