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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

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