Bustools

Introduction

Bustools is a program for manipulating BUS files for single cell RNA-Seq datasets.

For more information, please check its website: https://biocontainers.pro/tools/bustools and its home page on Github.

Versions

0.41.0

Commands

bustools

Module

You can load the modules by:

module load biocontainers
module load bustools

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 Bustools on our clusters:

#!/bin/bash
#SBATCH -A myallocation     # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=bustools
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
ml biocontainers bustools

bustools capture -s -o cDNA_capture.bus -c cDNA_transcripts.to_capture.txt -e matrix.ec -t transcripts.txt output.correct.sort.bus
bustools count -o u -g cDNA_introns_t2g.txt -e matrix.ec -t transcripts.txt --genecounts cDNA_capture.bus