8/7/24 DL

Script to calculate gene expression fold change within sigDC regions.

dchic_output/
tgif_output/
	sigDC results from dcHiC and TGIF-DC

de_output/
	differential expression (DEseq) results on H1 and endoderm 
	gene exression

1A_get_tgif_sig_dc_regions.sh
	Script to grab list of sigDC regions identified by TGIF-DC

tgif_sig_dc.bed
	Output file of preceding script

1B_get_dchic_sig_dc_regions.sh
	Script to grab list of sigDC regions identified by dcHiC

dchic_sig_dc.bed
	Output file of preceding script

2_group_genes.sh
	Script to group genes based on whether they are found within
	sigDC regions.

all_genes.bed
genes_NOT_within_dchic_sig_dc.bed
genes_NOT_within_tgif_sig_dc.bed
genes_within_dchic_sig_dc.bed
genes_within_tgif_sig_dc.bed
	Output files of preceding script	

compare_within_vs_not.py
	Compare gene expression fold change in sigDC regioins vs
	non-sigDC regions. Note this also generates the results
	and figure for Supp Fig 4B.

compare_within_vs_not.txt
tgif_within_sig_dc_vs_not.pdf
	Output files of preceding script

compare_tgif_vs_dchic.py
	Compare gene expression fold change in dcHiC sigDC regions
	vs TGIF-DC sigDC regions

tgif_vs_dchic.pdf
ttest.txt
	Ouputfiles of preceding script
