HOMER
Introduction
HOMER is a suite of tools for motif discovery and next-generation sequencing analysis. It is widely used for peak annotation, motif enrichment, and other analyses in ChIP-seq and related experiments.
Requirements
HOMER can be installed by the user on their home folder or project folder using conda environments. Therefore, requirements are usually handled automatically by the conda environments. We recommend users to install homer on their project storage since homer needs writing permissions to the user’s custom database repositories, and genomics databases could use significant storage. Moreover, conda environments can also use significant storage space depending on the number of packages installed on them. Therefore, if the user decides to install conda environment on their home folder, rather than a project folder, we recommend the users to consider the available storage capacity on their home folder before setting new conda environments.
Installation
# Requirement: Load conda modules before the following steps
# Run the code block below just once (ref: https://bioconda.github.io).
# This block of updates the channels and priorities on ~/.condarc
conda config --add channels bioconda
conda config --add channels conda-forge
conda config --set channel_priority strict
# Create a conda environment.
# We use prefix for separation of scopes between projects, but the user can omit that parameter.
# The --prefix parameter changes the location of the conda environment named seqtools to ~/biotools/
conda create -y --prefix ~/biotools/seqtools python=3.9.*
# Install homer
# Note: since a custom location was supplied (--prefix), we may need to set that parameter in other conda commands.
conda install -y --prefix ~/biotools/seqtools homer
Usage
The following code snippet could be used to create the SLURM batch script for running basic HOMER analyses: Adjust paths as needed for your project.
# Requirement: Load conda modules
# Path to Working Directory
myWorkDir="/u/$(whoami)/test-realm"
cd $myWorkDir
# Path to CONDA environment
CONDAENV="/u/$(whoami)/biotools/seqtools/"
## -- Input peak file (BED format, required)
## -- Reference genome (required, e.g. hg38 or mm10)
## -- Output directory (required)
# Run annotatePeaks with HOMER
conda run --prefix $CONDAENV annotatePeaks.pl input_peaks.bed hg38 > annotated_peaks.txt