spaceranger
Link to section 'Introduction' of 'spaceranger' Introduction
Spaceranger is a set of analysis pipelines that process Visium Spatial Gene Expression data with brightfield and fluorescence microscope images.
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.
Link to section 'Versions' of 'spaceranger' Versions
- 1.3.0
- 1.3.1
- 2.0.0
Link to section 'Commands' of 'spaceranger' Commands
- spaceranger
Link to section 'Module' of 'spaceranger' Module
You can load the modules by:
module load biocontainers
module load spaceranger
Link to section 'Example job' of 'spaceranger' 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 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