BET-seq analysis repository

This repository contains all the code to perform the analyses described in the Le, et al. manuscript describing MITOMI sequencing-based analysis of Pho4 and Cbf1 core binding site flanking sequences (BET-seq). This pre-print of the manuscript can be found on bioRxiv here and the final PNAS published version can be found here.

The following files are in this root directory:

• GEO_submission.xls - Excel spreadsheet with information for GEO submission of raw datasets
• setup.R - Code to setup necessary datasets and variables for full analysis
• Main_Figures.Rmd - Code to generate all of the figures in the main text
• SI.Rmd - Code to generate all figures and tables in the supporting information
• README.md - This README
• data - All of the processed data files (not included in this repo, data files can be found on Figshare)
• data_processing.py - Script to process raw fastq files
• figures - All of the final typeset figures from the main text
• images - All of the subplot/subfigure images
• neural_network - Code to run the neural network model
• simulations - Code to run assay parameterization simulations