8/7/24 DL

Scripts to annotate TGIF-DC clusters as A and B comaprtments
with GC content in mouse neural diff data

1_get_all_regions.sh
	script to make a bed file of all 100kb regions
	input: bed/
	output: all_regions.bed

2_get_nucleotide_profile.sh
	script to calcualte nucleotide profile (e.g. GC%)
	in each 100kb region
	input: mm10.fa, mm10.fa.fai
	output: nucleotide_profile.txt

3_get_mean_gc_per_cluster.py
	script to get mean GC% in each TGIF-DC cluster

4_annotate_cluster.py
	script to assign each cluster to A or B compartment
	based on GC%

5A_plot_gc_per_cluster.py
	script to visualize GC% per cluster

5B_plot_gc_per_compartment.py
	script to visualize GC% per compartment

tgif_output/
	output files from TGIF-DC

mean_gc_per_cluster/
	output files from script 3

annotated/
	output files from script 4

figures/
	output files from script 5A and B

