Single-Cell RNA-seq Analysis with CellRanger and Seurat

Author: Kevin Chau

Snakemake pipeline for single-cell RNA-seq analysis using cellranger and Seurat.

Usage

Included is a convenient conda environment description for ease-of-use and replicability. Please call

conda env create -f conda.yaml
source activate seurat

to initialize this environment prior to running the pipeline

Since downstream Seurat analysis requires some custom parameter inputs, this pipeline is divided into several parts:

1. Subworkflow: data_setup
   • CellRanger is used to quantify the RNA-seq data and an initial Seurat object is initialized per sample.
   • Browse the results of this portion of the pipeline and tune the respective parameters in data_setup/config.yaml; details are outlined in the file
2. Main Workflow
   • This Seurat object is then processed utilizing user-defined parameters in config.yaml.
   • Many scripts from scripts are replicated in user_analysis. This directory is provided as a convenient workspace for the user.

Initial counts and setup (data_setup)

Run this pipeline first to generate initial Seurat object. User should inspect data/{sample_id}/violin_and_scatter.pdf and set nUMI and percent_mito in config.yaml as necessary.

Automated Seurat analysis (main)

After modifying config.yaml, the user may run this pipeline to integrate multiple single-cell analyses and perform preliminary analyses.