8/7/24 DL

Scripts to measure GC content in annotated AB compartments
from H1-endoderm data 

1_get_all_regions.sh
	script to collect all 100kb regions
	input: bed/
	output: all_regions.bed

2_get_nucleotide_profile.sh
	script to get GC% in each 100kb region
	input: hg38.fa, hg38.fa.fai
	output: nucleotide_profile.txt

3_plot_gc_percentage.py
	script to visualize GC%

bed/
	bed files of 100kb regions

annotated/
	TGIF-DC clusters annotated as compartments

endoderm_gc_content.pdf
endoderm_gc_content.txt
endoderm_gc_per_chrom.pdf
H1_gc_content.pdf
H1_gc_content.txt
H1_gc_per_chrom.pdf
	output from script #3
