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# Scripts for CAD snATAC data analysis

# "Single-nucleus chromatin accessibility profiling highlights regulatory mechanisms of coronary artery disease risk"

This repo contains all the data analysis scripts in the manuscript "Single-nucleus chromatin accessibility profiling highlights regulatory mechanisms of coronary artery disease risk". In the following repo, 1_snATAC_analysis.r includes scripts for the single nucleus ATAC-seq data analysis, 2_scRNA_analysis.r includes scripts for the single cell RNA-seq data analysis, and 3_SVMpipeline/ and 4_RASQUAL_caQTL/ folders include various scripts for the variant effect predictions and allele-specific based caQTL mapping analyses using snATAC-seq peaks, respectively. See the details in the sections below. 

This repo contains all the data analysis scripts in the manuscript "Single-nucleus chromatin accessibility profiling highlights regulatory mechanisms of coronary artery disease risk". In the following repo, 1_scATAC_analysis.r includes scripts for the single nucleus ATAC-seq data analysis, 2_scRNA_analysis.r includes scripts for the single cell RNA-seq data analysis, and 3_SVMpipeline/ and 4_RASQUAL_caQTL/ folders include various scripts for the variant effect predictions and allele-specific based caQTL mapping analyses using snATAC-seq peaks, respectively. See the details in the sections below. 

## 0. Requirements

The following environments/packages are required to run the scripts. 

Single cell data analysis (snATAC_analysis.r and scRNA_analysis.r)

Single cell data analysis (scATAC_analysis.r and scRNA_analysis.r)

- R v4.0

- ArchR v1.0.1

- Seurat v4.0.0

- two annotation data [hg38.fa](https://www.dropbox.com/s/el46t6onl67ejhh/hg38_clean.fa?dl=0) and [hg38.chrom.sizes](https://www.dropbox.com/s/6pf8473bot9wxlv/hg38.chrom.sizes?dl=0)

## 1. single nucleus ATAC-seq (snATAC) data analysis

All the scripts for the snATAC data analysis were included in the 1_snATAC_analysis.r

All the scripts for the snATAC data analysis were included in the 1_scATAC_analysis.r

The snATAC data were generated for this study and pre-processed with 10x cellranger-atac pipeline (v1.2.0, with default parameters). The output files from the cellranger-atac pipeline were used as the input for the script. The script contains following parts.

- basicQC