#!/bin/bash

# Define your variables
PEAK_FILE="~/Public_html/MergedChipseq_peaks.fa"
GENOME="hg38"
MOTIF_DIR="MotifOutputDirectory"
MOTIF="~/Public_html/AR_MotifOutput/knownResults/known5.motif"
OUTPUT_FILE="motif5_output.txt"

# Run findMotifsGenome.pl to find the motif in peaks
findMotifsGenome.pl "$PEAK_FILE" "$GENOME" "$MOTIF_DIR" -find "$MOTIF" > "$OUTPUT_FILE"

echo "Motif search completed. Results saved to $OUTPUT_FILE"