eRNA_YRI_paper_code

Overview

This repository contains the source code and example data to reproduce the results described in the manuscript entitled "Population-scale study of eRNA transcription reveals bipartite functional enhancer architecture"

This repository contains the following two folders:

• TRE_identification folder contains the code and examples to identify transctibe regulatory elements (TREs).
• variant_alignment folder contains the code used to account for mappability and reference allele bias using allele-specific mapping.

Prerequisites

To use this repository, the following software tools need to be installed and should be accessible from your default path. The software version indicates the version used in our experiments. Other versions may work, but the same version may be required for a complete reproducbility.

• bedtools (v2.28)
• bowtie (v1.2.2)
• tabix (v1.7-2)
• R (v3.6.1)
• samtools(v1.9)
• git (v2.24.3)
• wget (v1.20.1)

Getting Started

Clone the repository

First, clone the repository with the following commands

## clone the repository
git clone https://github.com/hyunminkang/eRNA_YRI_paper_code.git
## change the working directory
cd eRNA_YRI_paper_code

Download the example

Second, download the example data (1.2GB) from our FTP site using the following commands

## your current working directory must be eRNA_YRI_paper_code
sh download.sh

The download may take several minutes, so please be patient.

Review README and run the codes

For each subdirectory, there is a README.txt file. Review the file information carefully to understand the expected behavior.

To run TRE_identification, use the following commands:

## your current working directory must be eRNA_YRI_paper_code
cd TRE_identiciation
sh sh/make.PROcap.eTSS.sh 
cd .. ## move to the original directory

To run variant_alignment, use the following commands:

## your current working directory must be eRNA_YRI_paper_code
cd variant_alignment
sh sh/make.sh
cd .. ## move to the original directory

You may modify the variables to apply the scripts to other samples

Reference

To cite our repository, please cite the following information:

Kristjánsdóttir K, Kwak Y, Tippens ND, Lis JT, Kang HM, Kwak H. Population-scale study of eRNA transcription reveals bipartite functional enhancer architecture. bioRxiv. 426908.