Spaceranger

Introduction

Spaceranger is a set of analysis pipelines that process Visium Spatial Gene Expression data with brightfield and fluorescence microscope images.

For more information, please check its | Docker hub: https://hub.docker.com/r/cumulusprod/spaceranger/tags and its home page: https://support.10xgenomics.com/spatial-gene-expression/software/pipelines/latest/what-is-space-ranger.

Versions

1.3.0
1.3.1
2.0.0

Commands

spaceranger

Module

You can load the modules by:

module load biocontainers
module load spaceranger

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 Spaceranger on our clusters:

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

module --force purge
ml biocontainers spaceranger

spaceranger count --id=sample345 \ #Output directory
               --transcriptome=/opt/refdata/GRCh38-2020-A \ #Path to Reference
               --fastqs=/home/jdoe/runs/HAWT7ADXX/outs/fastq_path \ #Path to FASTQs
               --sample=mysample \ #Sample name from FASTQ filename
               --image=/home/jdoe/runs/images/sample345.tiff \ #Path to brightfield image
               --slide=V19J01-123 \ #Slide ID
               --area=A1 \ #Capture area
               --localcores=8 \ #Allowed cores in localmode
               --localmem=64 #Allowed memory (GB) in localmode