The information landscape of human transcription factor and DNA interactions

A companion repository

Ricardo D’Oliveira Albanus, Yasuhiro Kyono, John Hensley, Arushi Varshney, Peter Orchard, Jacob O. Kitzman, Stephen C. J. Parker

Description

This repository will allow you to generate all the main figures from our manuscript. If you only want to use BMO, please refer to the official BMO repository.

Usage

Browsing processed results

1. Download the full processed data from zenodo and place it at the root of the cloned repository:

wget https://zenodo.org/record/3478583/files/chromatin_information_manuscript_data.tar.gz
tar -xzvf chromatin_information_manuscript_data.tar.gz

2. The notebooks folder contains a Rmd (R Markdown) file for each set of analyses. Just open these files in RStudio and knit the html output.

Generating results from scratch

Go to each of the analyses subfolders in order and run the commands described in the README.

Software requirements

Using our conda environment

Assuming that you have a Linux 64-bit system, download and install Anaconda 3:

wget https://repo.continuum.io/archive/Anaconda3-5.0.1-Linux-x86_64.sh
bash Anaconda3-5.0.1-Linux-x86_64.sh

Create the base environment:

conda env create --file env/base.yml
source activate chromatin_information

This will provide most of the command line software (python, R, samtools, etc.)

Install other software

Fetch the necessary R packages

Rscript scripts/install_dependencies.R

Other required software can be found following the links below. The versions we used are in parentheses.

• CENTIPEDE (1.2)
• DNase2TF (1.0)
• HINT (0.12.1, RGT 1.1.1)
• PIQ (1.3)
• ngsplot (2.63)

We bundled the core BMO scripts here, but if you wish to use it in your own projects, please refer to the official BMO repository.

Manually installing the core dependencies included in conda environment

In case you cannot use the environment, below are the core dependencies:

• R (3.5.1)
• Python (3.5.3)
• Rstudio (1.1.456). Required for the RMarkdown notebooks.
• bedtools (2.26.0)
• samtools (1.9)
• MACS2 (2.1.1.20160309)
• Snakemake (5.5.0)
• Slurm (16.05.09) or some other job scheduler. The cluster config files here are set up for slurm.

Contact

• For questions directly about the paper, the corresponding author is Dr. Stephen C.J. Parker (scjp@umich.edu).
• If anything here is or feels broken, or if you just have questions regarding how to set up the analyses, contact Ricardo Albanus directly at dricardo@wustl.edu or create an Issue in this repository.