3/6/23 DL 

For each of the bin containing any of the top 100 most transcriptionally active HERV-H sites,
get the boundary score within that bin, and plot the boudnary score mean/distribution
for each timepoint

all_hervh_sites_sorted_by_txn_level.bed
	contains all HERV-H sites sorted by transcription level. Provided by Yanxiao Zhang and Bing Ren.

somatic_chro_regions_with_top100_txn_hervh_sites.csv
	list of genomic bins in somatic chromosomes containing any of the top 100 transcriptionally
	active HERV-H sites

get_neighborhood_score.py
	script to grab the TGIF boundary score for each of the bins in somatic_chro_regions_with_top100_txn_hervh_sites.csv
  (+ its neighboring bins in a certain radius, but not used for further analysis)

neighborhood_score.txt
	output of get_neighborhood_score.py
		
figure_hervh_site_score.py
	script to generate barplot of boundary scores in the top transcriptionally active HERV-H
	site containing bins in each timepoint during differentation

figure_hervh_site_score.pdf
	output of figure_hervh_site_score.py

visualize/
	scripts and outputs for visualizing region of interest
