TPMCalculator

Introduction

TPMCalculator quantifies mRNA abundance directly from the alignments by parsing BAM files.

Detailed usage can be found here: https://github.com/ncbi/TPMCalculator

Versions

0.0.3
0.0.4

Commands

TPMCalculator

Module

You can load the modules by:

module load biocontainers
module load tpmcalculator

Example job

Warning

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