GRS_SC10X

A pipeline for 10X cellranger

Aim: to streamline and simplify 10X cellranger process

Overview

GRS_SC10X to simplify and streamline cellranger process based on different chemistry.

Dependencies

Requires: snakemake>=6.0

Installation

NIH_HPC(Biowulf)

Please clone this repository using the following commands:

# Clone Repository from Github
git clone https://github.com/OpenOmics/GRS_SC10X.git
cd GRS_SC10X/

# Get usage information
python ./grs_sc10x.py -h

Execution-fastq

python grs_sc10x.py run \
--title sc_gex_fastq \
--input /data/RTB_GRS/ActiveProjects/user_project/cellranger_mkfastq_0204_AHLYKTBGXM/HLYKTBGXM/ \
--input-type fastq \
--host mouse \
--design /data/RTB_GRS/ActiveProjects/GRS_0088_Wishart/wishart_sample_design.csv \
--output /data/$USER/Test_Space/GRS_SC10X \
--mode slurm
##
cd /data/$USER/Test_Space/GRS_SC10X/sc_gex_fastq
sbatch --cpus-per-task=16 --mem=16g --time=24:00:00 sc_gex_fastq_GRS_SC10X_execution.sh

Execution-bcl

python grs_sc10x.py run \
--title sc_gex_bcl \
--input /data/RTB_GRS/SequencerRuns/GRS_0088_Wishart/230324_NS500353_0204_AHLYKTBGXM/ \
--input-type bcl \
--host mouse \
--design /data/RTB_GRS/ActiveProjects/user_project/wishart_sample_design.csv \
--output /data/$USER/Test_Space/GRS_SC10X \
--sample-sheet /data/RTB_GRS/ActiveProjects/user_project/cellranger_mkfastq_0204_AHLYKTBGXM/CellRanger_SampleSheet_GRS_0088.csv \
--mode slurm
##
cd /data/$USER/Test_Space/GRS_SC10X/sc_gex_bcl
sbatch --cpus-per-task=16 --mem=16g --time=24:00:00 sc_gex_bcl_GRS_SC10X_execution.sh

References

^{1. Koster, J. and S. Rahmann (2018). "Snakemake-a scalable bioinformatics workflow engine." Bioinformatics 34(20): 3600.}