#!/bin/bash

# Set the MEME executable path and input/output files
MEME_EXEC="/home/litd/meme/bin/meme"
INPUT_FILE="MergedChipseq_peaks.fa"
OUTPUT_DIR="meme_output"

# Create the output directory if it doesn't exist
mkdir -p "${OUTPUT_DIR}"

# Run MEME analysis
"${MEME_EXEC}" "${INPUT_FILE}" -oc "${OUTPUT_DIR}" -dna -nmotifs 5

echo "MEME analysis completed. Results are saved in ${OUTPUT_DIR}."