#!/bin/bash

# Genome
GENOME=hg38

# Input peak files
PEAKS=(
    "LNCaP_FOXA1_DHT100nm_rep1.bed"
    "LNCaP_FOXA1_DHT100nm_rep2.bed"
    "LNCaP_FOXA1_DMSO_rep1.bed"
    "LNCaP_FOXA1_DMSO_rep2.bed"
)

# Output folder
mkdir -p homer_results

# Loop and run HOMER
for file in "${PEAKS[@]}"; do
    name=$(basename "$file" .bed)
    outdir="homer_results/${name}"

    echo "Running HOMER: $file → $outdir"

    findMotifsGenome.pl "$file" $GENOME "$outdir" -p 8

done

echo "Done! Results saved in homer_results/"