chipseq analysis tutorial

End-to-end ChIP-seq analysis pipeline for USF2 (as an example) including alignment, peak calling, annotation, and visualization

Environment Setup & Verification

⚠️ Please complete this section before running the pipeline.

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Step 1: Create and activate environment

conda create -n homer_env python=3.10 -y
conda activate homer_env

Step 2: Configure conda channels

conda config --env --add channels defaults
conda config --env --add channels bioconda
conda config --env --add channels conda-forge
conda config --env --set channel_priority strict

Step 3: Install required tools

conda install -y wget samtools ucsc-bedgraphtobigwig ucsc-fetchchromsizes ucsc-bedtobigbed sra-tools trim-galore bedtools picard bwa deeptools

Step 4: Create a directory for HOMER installation

mkdir -p $CONDA_PREFIX/homer
cd $CONDA_PREFIX/homer

Step 5: Download the HOMER installation script

wget http://homer.ucsd.edu/homer/configureHomer.pl

Step 6: Install HOMER with default settings

perl configureHomer.pl -install

Step 7: Add HOMER executables to the PATH in this conda environment

echo 'export PATH=$CONDA_PREFIX/homer/bin:$PATH' >> $CONDA_PREFIX/etc/conda/activate.d/homer.sh

Step 8: We deactivate + reactivate to reload environment so HOMER is added to PATH

conda deactivate
conda activate Env_Homer

Step 9: Display all available reference genomes in HOMER

perl configureHomer.pl -list

Step 10: Install human genome (hg38) for our analysis

perl configureHomer.pl -install hg38