single-cell Perturb-Seq pipelines

This repository includes

• 1. Hashtag data processing pipeline to quantify tag UMIs in individual cells and binarize the count table using Gaussian Mixed Modeling for model-based clustering;
• 2. Guide RNA data (a novel design of dual guides in vector backbone) processing pipeline to quantify guide UMIs in individual cells and binarize the count table using Gaussian Mixed Modeling;
• 3. Benchmarking of a test guide RNA dataset generated from 10x Genomics platform. Both in-house guide processing tool and Cellranger3 were used for comparison.

Directory contents

• Hashtag pipeline: A folder with RUST executable file.
• Guide RNA pipeline: A folder with RUST executable file.
• Benchmarking of guide RNA data: A folder with benchmarking results.

Installation of hashtag_tool and guiderna_tool

cd ~
wget https://github.com/gaofan83/single_cell_perturb_seq/releases/download/v.1.0.0/v.1.0.0.tar.gz
tar -xvzf v.1.0.0.tar.gz
chmod +x single_cell_perturb_seq/hashtag/hashtag_tool
chmod +x single_cell_perturb_seq/guiderna/guiderna_tool
export PATH=~/single_cell_perturb_seq/hashtag/:$PATH
export PATH=~/single_cell_perturb_seq/guiderna/:$PATH

Citation

Please cite the following paper when using this software:
W Zhou, F Gao, M Romero-Wolf, S Jo, EV Rothenberg. Science Immunology (2022)
"Single-cell deletion analyses show control of pro–T cell developmental speed and pathways by Tcf7, Spi1, Gata3, Bcl11a, Erg, and Bcl11b." 

An online resource to understand the basics of 10X single-cell perturb-seq

Sarah Teichmann's group at EMBL-EBI / Wellcome Trust Sanger Institute