Salmon¶
Salmon is a tool for transcript quantification from RNA-seq data.
Salmon is available as a module on Apocrita.
Usage¶
To run the latest 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 ${NSLOTS}
.
Example job¶
Serial job¶
Here is an example job running on 1 core and 1GB total memory:
#!/bin/bash #$ -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}