Single nuclei RNA seq processing pipeline (2023 version)

Managed by @aladyeva-research

Repository with single nuclei RNAseq initial (QC + integration) data analysis pipeline

Stages:

1. "Soup" removal
2. Doublets identification
3. QC filtering
4. Preprocessing

Prerequisites:

Create conda environment (use mamba for faster installation)

CONDA_ENV=<conda_name>
conda env create -n $CONDA_ENV --file snakemake/envs/pipeline_env.yml
conda activate $CONDA_ENV
Rscript snakemake/envs/install_packages.R

Populate data (create symlinks)

chmod +X scripts/populate_data.sh
./scripts/populate_data.sh

Edit config.yaml

vim snakemake/config/config.yaml

Run pipeline

Dry-run

snakemake -pr -s snakemake/run_pipeline.smk --configfile snakemake/config/config.yml \
    -c 4 --use-conda --conda-frontend mamba --rerun-incomplete --scheduler=greedy --dry-run

Real run

snakemake -pr -s snakemake/run_pipeline.smk --configfile snakemake/config/config.yml \
    -c 4 --use-conda --conda-frontend mamba --rerun-incomplete --scheduler=greedy