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 ${NSLOTS}.
Example job¶
Serial job¶
Here is an example job running on 1 core and 1GB of memory:
#!/bin/bash
#$ -cwd
#$ -j y
#$ -pe smp 1
#$ -l h_rt=1:0:0
#$ -l h_vmem=1G
module load salmon
salmon index -t transcripts.fasta \
-i transcripts_index \
-p ${NSLOTS}
salmon quant -i transcripts_index \
-l A \
-1 file1.fastq \
-2 file2.fastq \
--validateMappings \
-o transcripts_quant \
-p ${NSLOTS}