# a basic example
python ../PePr.py -i input_rep1.bed,input_rep2.bed -c chip_rep1.bed,chip_rep2.bed -f bed -s 48,46 -w 180 -n my_test_run
# running without normalizatiom 
python ../PePr.py -i input_rep1.bed,input_rep2.bed -c chip_rep1.bed,chip_rep2.bed -f bed -s 48,46 -w 180 -n no_normalization --custom_normalization NO
#running without input samples 
python ../PePr.py -c chip_rep1.bed,chip_rep2.bed --chip2 input_rep1.bed,input_rep2.bed -f bed -s 48 -w 180 -n no_input_run --diff
