cellbender
Link to section 'Introduction' of 'cellbender' Introduction
Cellbender is a software package for eliminating technical artifacts from high-throughput single-cell RNA sequencing (scRNA-seq) data.
For more information, please check its website: https://biocontainers.pro/tools/cellbender and its home page on Github.
Link to section 'Versions' of 'cellbender' Versions
- 0.2.0
- 0.2.2
Link to section 'Commands' of 'cellbender' Commands
- cellbender
Link to section 'Module' of 'cellbender' Module
You can load the modules by:
module load biocontainers
module load cellbender
Link to section 'Example job' of 'cellbender' 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 Cellbender on our clusters:
#!/bin/bash
#SBATCH -A myallocation # Allocation name
#SBATCH -t 10:00:00
#SBATCH -N 1
#SBATCH -n 24
#SBATCH --job-name=cellbender
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out
module --force purge
ml biocontainers cellbender
cellbender remove-background \
--input cellranger/test_count/run_count_1kpbmcs/outs/raw_feature_bc_matrix.h5 \
--output output_cpu.h5 \
--expected-cells 1000 \
--total-droplets-included 20000 \
--fpr 0.01 \
--epochs 150