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?
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:
Can you help me?