cellSNP

Introduction

cellSNP aims to pileup the expressed alleles in single-cell or bulk RNA-seq data, which can be directly used for donor deconvolution in multiplexed single-cell RNA-seq data, particularly with vireo, which assigns cells to donors and detects doublets, even without genotyping reference.

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

Versions

• 1.2.2

Commands

• cellsnp-lite

Module

You can load the modules by:

module load biocontainers
module load cellsnp-lite

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 cellSNP on our clusters:

#!/bin/bash
#SBATCH -A myallocation     # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 8
#SBATCH --job-name=cellsnp-lite
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
ml biocontainers cellsnp-lite

cellsnp-lite -s sample.bam -b barcode.tsv -O cellsnp_out -p 8 --minMAF 0.1 --minCOUNT 100