Salmon¶
Salmon is a tool for transcript quantification from RNA-seq data.
Salmon is available as a module on Apocrita.
Usage¶
To run the default installed version of Salmon, simply load the salmon
module:
$ module load salmon
$ salmon --help
Usage: salmon -h|--help or
salmon -v|--version or
salmon -c|--cite or
salmon [--no-version-check] <COMMAND> [-h | options]
Commands:
index : create a salmon index
quant : quantify a sample
alevin : single cell analysis
swim : perform super-secret operation
quantmerge : merge multiple quantifications into a single file
Number of threads
By default, Salmon will run multi-threaded on all available cores. To
prevent overloading a compute node, you should override this by passing
the p / --threads parameter with the value of ${SLURM_NTASKS} on commands
which offer this option.
Example job¶
Serial job¶
Here is an example job running on 1 core and 1GB of memory:
#!/bin/bash
#SBATCH -n 1 # (or --ntasks=1) Request 1 core
#SBATCH --mem-per-cpu=1G # Request 1GB RAM per core
#SBATCH -t 1:0:0 # Request 1 hour runtime
module load salmon
salmon index -t transcripts.fasta \
-i transcripts_index \
-p ${SLURM_NTASKS}
salmon quant -i transcripts_index \
-l A \
-1 file1.fastq \
-2 file2.fastq \
--validateMappings \
-o transcripts_quant \
-p ${SLURM_NTASKS}