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# Topologically associating domains and their role in the evolution of genome structure and function in Drosophila
# Genome Research, 2021
# Information on the files in this repository
# Contact: liaoyi1022@hotmail.com,  jje@uci.edu
# The souce code and the corresponding precessed files also available at the following GitHub repository: https://github.com/yiliao1022/TADEvoDrosophila 
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## bin
Perl Scripts

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## Fig 1  

TADannotationDpse.sh # TAD annotaion using HiCExplorer, arrowhead, and Armatus for Dpse whole body sample
TADannotationDmel.sh # TAD annotaion using HiCExplorer, arrowhead, and Armatus for Dmel three cell lines 
Fig1_epigenetic_marks.sh # walkthrough for epigenetic marks (CTCF, BEAF, ATACseq, H3k4me3, and H3K27me3) analysis
Figure1A.sh # TAD plot
Figure1B_VennDiagram_TAD.r # Overlap TADs with three tools
Figure1C_TADsize_distribution.r # TAD size distribution for three tools
Figure1DEF.r # Epigenetic marks around TAD boundaries


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## Table 1

Table1.boundary.sh # Evaluation of TAD boundary conservation 
Table1.TAD.sh # Evaluation of TAD body conservation


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## Fig 2

Fig2A.circos.sh 	# circos plot
Figure2C_Conservation_cellTypes.r # Overlap of TADs across three Dmel cell lines.
Figure2DE.upset.r # Upset plot
Figure2FGH.r # TAD size analysis


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## Fig 3
Figure3_prop_test.R		# Conservation of different classes of TAD boundaries analysis


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## Fig 4
Figure4_EucPeaD.r  # Measure gene expression divergence using Euclidean distance and Pearson’s correlation coefficient distance
GeneExpression_versus_TAD.sh # walkthrough for gene-versus-TAD analysis


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## Fig 5
17SpeciesSynteny_walkthrough.sh 	# Chromosomal rearrangements and TAD analysis wallthrough
Figure5_CD.r 		# Figure5 c and d plot


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## Fig 6
SVcalling_walkthrough.sh # SV variants identification
Figure6BC_SV_Bar.r  #Fig6 b and c plot
Figure6D_Pop_SFS.R  #Fig6 d plot
Figure6E_Dsim_SFS.R #Fig6 e plot  
Figure6G_ODD_ratios.r #Fig6 g plot 
Figure6F_Purifying_matric.r #Fig6 F plot
Figure6HI_.peak.2.r #Fig H and I plot


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## Supplemental Fig
SupplementalFigureS14_permulation_insertion_deletion.r # Supplemental Figure S14
SupplementalFigS15_permulation_CNV_LTR_LINE_DNA.r  # Supplemental Figure S15
