Emotif Alpha: A multi-omic DNA motif discovery and selection pipeline

Installation

This pipeline is developed in python 2. Should only work in Linux system.

1. GimmeMotifs

GimmeMotifs is a collection of motif discovery tools. The most straightforward way to install GimmeMotifs (https://github.com/simonvh/gimmemotifs ) is:

conda create -n motif_py2 python=2 gimmemotifs

2. DME

git clone https://github.com/smithlabcode/dme

cd dme

https://github.com/smithlabcode/smithlab_cpp.git

module load gcc/6.3.0 (specifically for stjude HPC)

make

./dme2 (you should be able to see the help message)

Next, add dme2 to your env var.

export PATH=$PATH:/PATH_TO_DME2/

3. biopython sklearn joblib

Sometimes installing a python package can upgrade your python 2 to python 3 automatically, be aware what is installed.

conda install -c anaconda biopython

conda install -c anaconda scikit-learn

conda install -c anaconda joblib

conda install -c bioconda genomepy

genomepy install hg19 UCSC --annotation

4. install Emotif

git clone https://github.com/YichaoOU/Emotif_Alpha.git

cd Emotif_Alpha

Note that you should be in the conda env where you have all the required library installed, e.g., motif_py2

python setup.py install

Example Usage:

1. Copy a sample configuration file

Emotif_alpha -copy

2. Run motif discovery ensemble

Emotif_alpha -f sample.md

By default, the jobID (i.e., a folder that contains all motif discovery results) is [Username]_Emotif_alpha_[Date]

Other Dependencies

(1) R ggplot2 (https://github.com/hadley/ggplot2 )

(2) MEME suite (http://meme-suite.org/doc/install.html?man_type=web ) You will use meme, meme2images, fimo, and mast.

(3) JAVA, to run DECOD

FAQ:

(1) wrong GimmeMotifs command? Depends on the GimmeMotifs version, the command in the motif_discovery.py may not be correct. (2) can't find dme2 command? Please put the dme2 in your $PATH.

High-level Workflow