souporcell
Link to section 'Introduction' of 'souporcell' Introduction
souporcell is a method for clustering mixed-genotype scRNAseq experiments by individual.
Home page: https://github.com/wheaton5/souporcell
Link to section 'Versions' of 'souporcell' Versions
- 2.0
Link to section 'Commands' of 'souporcell' Commands
- check_modules.py
- compile_stan_model.py
- consensus.py
- renamer.py
- retag.py
- shared_samples.py
- souporcell.py
- souporcell_pipeline.py
Link to section 'Module' of 'souporcell' Module
You can load the modules by:
module load biocontainers
module load souporcell
Link to section 'Example job' of 'souporcell' 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 souporcell on our clusters:
#!/bin/bash
#SBATCH -A myallocation # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 8
#SBATCH --job-name=souporcell
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out
module --force purge
ml biocontainers souporcell
souporcell_pipeline.py -i A.merged.bam \
-b GSM2560245_barcodes.tsv \
-f refdata-cellranger-GRCh38-3.0.0/fasta/genome.fa \
-t 8 -o demux_data_test -k 4