salmon
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
Link to section 'Versions' of 'salmon' Versions
- 1.5.2
- 1.6.0
- 1.7.0
- 1.8.0
- 1.9.0
Link to section 'Commands' of 'salmon' Commands
- salmon index
- salmon quant
- salmon alevin
- salmon swim
- salmon quantmerge
Link to section 'Module' of 'salmon' Module
You can load the modules by:
module load biocontainers
module load salmon
Link to section 'Example job' of 'salmon' Example job
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