Analysis of Surajit Dhara's paper (Pancreatic cancer prognosis is predicted by a novel ATAC-array technology for assessing chromatin accessibility):
This repository contains the analysis scripts for ATAC-seq and ATAC-array analysis of the research project published and linked here
ATAC-seq analysis pipeline and processing scripts authored by Sagar Chhangawala ([email protected])
As_Atlas_creation.R is the script used to generate the global atlas of reproducible chromatin peaks mentioned in the paper.
ATAC-array analysis java code authored by Bo Curry and implemented by Himanshu Chintalapudi for Surajit Dhara's research project.
The pipeline (src/ATACanalysis/ATACanalysis.java) is used to read the FE files, normalize and average the region data, and classify the samples.
It produces a file "ATACregionLRs.txt" which can be further processed through downstream analysis R scripts for visualization.
Input FE files in the folder 'Ag_FE_data' and more info in config/README.txt
Requirements:
JAVA - version 1.8
Usage:
java ATACanalysis.ATACanalysis ATACanalysis/config/ Ag_FE_data/*