Required module:
	tensorflow_gpu = 1.13.1
	keras = 2.2.0
	numpy = 1.16.3
	samtools=1.9

OS requirement: linux based system. Recommend Ubuntu 18.04 LTS 

Memory requirement: >=16GB

GPU Memory requirement: >=8GB

phastCons46way file can be download from http://hgdownload.soe.ucsc.edu/goldenPath/hg19/phastCons46way/placentalMammals/ , all file like chr1.phastCons46way.placental.wigFix.gz need to be download and extract to phastCons46way_placental directory.

You need to specify the paths for the bed file in "DmiRT_test.py" that contains the area of interested, the area of interested should be 1kbps length.

And the path bed formatted DNASE file and H3K4me3 file. If you need to convert these file from bam to bed, we provide a short script(convert_bam_to_bed.py) here as well. You need to install samtools in order to use this script.

For DmiRT_test.py:
	input_bed_file_path correspond to the input bed file path, 
	DNASE_bed_file_path correspond to the DNASE bed file path,
	H3K4me3_bed_file_path correspond to the H3K4me3 bed file path

For convert_bam_to_bed.py:
	bam_file_path  is the path of bam file that you want to convert into bed.