Quantify ecDNA in 10X single-cell ATAC (scATAC-seq) sequencing.
Owen Chapman University of California San Diego
This module estimates the abundance of a known extrachromosomal circular DNA sequence (ecDNA) in single cells from 10x Genomics scATAC-seq data. The approach counts reads mapping to the ecDNA region, then compares this value to an empirically derived null distribution of read coverage elsewhere in the genome. ecDNA+ cells are identified which have significantly greater scATAC-seq coverage than expected by the null.
To use this module, the following are required:
- Single-cell or spatial sequencing data such as that produced by the 10X Genomics single-cell ATAC-seq (scATAC-seq) workflow.
- Genomic co-ordinates of an ecDNA amplification in your sample. We have used AmpliconArchitect to generate these data from bulk WGS.
Currently, this module is a bash script with python 3 dependencies. Compatible with Linux (Ubuntu 16) and Mac OS (M1) operating systems. Future versions may include a proper package and containerized Docker version if I ever get around to it.
Dependencies:
- python 3
-- argparse
-- gzip
-- pyranges
-- pandas
-- seaborn
-- matplotlib
-- statsmodels - bedtools 2
Copy the example config file to your desired project directory and edit to point to paths of the required files. Set the $ECQ_HOME environment variable to the root directory for this repository, eg. Users/ochapman/software/ecdna-quant. Run using the command $ECQ_HOME/src/ecdna-quant config. See the test directory for a worked example.