WGD gene pair methylation level TADs boundary methylation level TADs boundary gene density Gene compartments judgment OE matrix generation Chromosome interaction-distance WGD gene pair contact score Gene pair contact frequency Conservative TADs analysis
TIPS

Function: Calculate the methylation level around the boundary of TADs.
Test data: chr_size.txt, TAD_list.txt, wgd_CG.txt, wgd_CHG.txt, wgd_CHH.txt, 60, 1000.
Download link of test file: https://github.com/yangxy2/3Dgenome-file/tree/main/web_test_file.
Input data description:
Chromosome size: No header; 2 columns, separated by tab; From left to right, each column represents chromosome name and chromosome length;
TADs list: No header; 3 columns, separated by tab; From left to right, each column represents chromosome name, start coordinate, end coordinate;
CG(/CHG/CHH) level: Methylation level data; The first row is the header, which is "Lachesis_group_ID Coordinate Value"; 3 columns, separated by tab; Each column represents the chromosome number, the base position of methylation on the chromosome, and the methylation level.
Window number: Number of windows around the TAD boundary (integer, half on left and right);
Window size: Size of each window(integer)