[file information]

*.rst3 has the processed data considering sonication
*.info has the output of GITTAR

seq.fa has the sequence data of all the probes
It has FASTA style 
">ENCODE_PROBENAME"
that match with the first column of rst3

to use trained HMM run
	./IntHMM.py test.fa
	The output are
	>seq_name
		tf : position (start, stop), probability



The experiment used in the manuscript are 
	./runChip_fp.py
	it does the cross-validation

Test histone modification
	./runHis.py

	the result file is on ./report directory