Question about TADs on fusion region

[YPGG1234]

Hello! Thanks for developing HiCExplorer.

Recently I have used hicexplorer (ver 3.7.2) to call TADs, I have Hi-C data and a genome of species A, as well as Hi-C data of its sister species B, in which species A experienced a chromosomal fusion event while species B did not. I aligned the Hi-C data of species A and B to the genome of species A separately and called TADs. I want to see if species A established TADs at the fusion position compared to species B.

I can see from the comparison of B species Hi-C data mapped to the A genome that there is no interaction between the two parts of chromosomes, but when zooming in to the fusion site, there is a large TAD at this location. The TAD pattern in A species is clearly different from that of B species, but it does not cross the fusion site. My current question is: can this indicate that A species has established more interactions after chromosome fusion compared to B species, and whether there has been a change in chromatin conformation in A species after chromosome fusion?

Here are commands:

hicBuildMatrix --samFiles hic.R1.bam hic.R2.bam --binSize 10000 --restrictionCutFile rest_site_positions.bed --restrictionSequence GATC --danglingSequence GATC --outFileName hicMatrix/10kb.sub.h5 --QCfolder hicMatrix/10kb_QC.sub --threads 5 --inputBufferSize 400000

hicCorrectMatrix correct -m hicMatrix/10kb.sub.h5 --filterThreshold -1.5 2.5 -o hicMatrix/10kb.corrected.h5

hicMergeMatrixBins --matrix hicMatrix/10kb.corrected.h5 --numBins 25 --outFileName hicMatrix/250kb.corrected.h5

hicFindTADs --matrix hicMatrix/250kb.corrected.h5 --minDepth 1000000 --maxDepth 2000000 --numberOfProcessors 4 --step 250000 --thresholdComparisons 0.05 --outPrefix TADs/250Kb.TADs --correctForMultipleTesting fdr

Can you help me?