scAVENGERS

Overview

scAVENGERS demultiplexes snATAC-seq data by genotype, referring to the variant information.

Execution

1. Installation

The command below clones the repository and installs dependencies.

wget https://github.com/kaistcbfg/scAVENGERS/archive/refs/tags/v1.0.0.tar.gz
tar -xvzf v1.0.0.tar.gz
conda env create -f scAVENGERS/envs/environment.yml

2. Setting parameters for scAVENGERS pipeline

Via the config file in yaml format, you can set parameters for the execution of the pipeline. The parameters include the path of the input and output data and settings for each program in the pipeline. The format is provided in config.yaml.

3. Running scAVENGERS pipeline

Below is a command to run the whole pipeline for demultiplexing. scAVENGERS require an indexed alignment file, an indexed reference genome file, and a line-seperated list of barcode sequences in a text file.

conda activate scavengers
$scAVENGERS_directory/scAVENGERS pipeline --configfile config.yaml -j $THREADS

4. Accessing the result

Running scAVENGERS pipeline results in a tab-delimited file. This result file clusters.tsv is structured like the below. To note, the format is compatible with the cluster result file generated from souporcell (https://github.com/wheaton5/souporcell).

column name	description
barcode	barcode sequence
status	status of the barcode sequence: singlet or doublet
assignment	cluster number where the barcode is assigned. Doublets are expressed in the form {n}/{n}.
log_prob_singleton	log singleton probability calculated by troublet
log_prob_doublet	log doublet probability calculated by troublet
cluster{n}	log likelihood of the assignment on cluster n.

Tutorial: demultiplexing human prefrontal cortex scATAC-seq data

First, prepare data by running the script below.

wget http://junglab.kaist.ac.kr/Dataset/scAVENGERS_example.tar.gz
tar -xvf scAVENGERS_example.tar.gz
cd scAVENGERS_example
gzip -d genome.fa.gz

Then, you can run the whole pipeline by running below:

$scAVENGERS_directory/scAVENGERS pipeline -j 10 --configfile config.yaml

Citation

Seungbeom Han, Kyukwang Kim, Seongwan Park, Andrew J Lee, Hyonho Chun, Inkyung Jung, scAVENGERS: a genotype-based deconvolution of individuals in multiplexed single-cell ATAC-seq data without reference genotypes, NAR Genomics and Bioinformatics, Volume 4, Issue 4, December 2022, lqac095, https://doi.org/10.1093/nargab/lqac095

Documentation

For further information, please refer to the documentation at https://scavengers.readthedocs.io/en/latest/.