tpmcalculator
TPMCalculator quantifies mRNA abundance directly from the alignments by parsing BAM files.
Detailed usage can be found here: https://github.com/ncbi/TPMCalculator
Link to section 'Versions' of 'tpmcalculator' Versions
- 0.0.3
- 0.0.4
Link to section 'Commands' of 'tpmcalculator' Commands
- TPMCalculator
Link to section 'Module' of 'tpmcalculator' Module
You can load the modules by:
module load biocontainers
module load tpmcalculator
Link to section 'Example job' of 'tpmcalculator' 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 tpmcalculator on our our clusters:
#!/bin/bash
#SBATCH -A myallocation # Allocation name
#SBATCH -t 10:00:00
#SBATCH -N 1
#SBATCH -n 12
#SBATCH --job-name=tpmcalculator
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out
module --force purge
ml biocontainers transdecoder
TPMCalculator -g Homo_sapiens.GRCh38.105.chr.gtf -b SRR12095148Aligned.sortedByCoord.out.bam