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.

Versions

0.2.0

Commands

cellbender

Module

You can load the modules by:

module load biocontainers
module load cellbender

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 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