Is there any way to obtain the regions within the neoTADs?

[AuraStephenson]

Hi, Xiaotao,

We are using NeoLoopFinder to identify neoTADs derived from SVs in our samples. We wanted to know if there is a way to obtain or calculate the coordinates (e.g., in a BED file) of the regions within the neoTADs, in order to analyze the genes and chromatin features that may be disrupted by these structures.

Many thanks!

[XiaoTaoWang]

Hi, sorry for the late response. Is the command neotad-caller what you were looking for?

[AuraStephenson]

Hello! Thank you for your response!
We use the neotad-caller command to call NeoTADs in our samples, but the output file contains the coordinates of the NeoTAD boundaries. We've explored some of them using "visualize," but as far as I’ve been able to understand, we need to build the image of each NeoTAD to identify the genes located within them.

I tried using the boundary coordinates along with the breakpoint coordinates to systematically determine the internal regions, but it’s still not entirely clear to me how to correlate both datasets, especially when dealing with inverted or complex SVs. We even have cases where up to three sections of chromosomes are involved in forming these structures (example.pdf).

Example in NeoLoopFinder:

A1 translocation 17 49.985.000 - X 88.215.000 + translocation X 87885000 - 17 39305000 - 17 50.680.000 17 40.200.000

NeoTAD identified:

chr17 39.390.000 39.400.000 chr17 50.110.000 50.120.000 A1,570000,1

Can you help me understand how I could get these regions from the outputs, we have several samples with a lot of NeoTADs identified so It would be of a lot of help if we were able to get a file with the exact fragments involved in the neoTADs formations in order to analyze patterns in all of our samples.

Thank you very much

[XiaoTaoWang]

Hi,

The output format of neotad-caller is identical to that of neoloop-caller. Therefore, one way to visualize neo-TADs using NeoLoopFinder is to use the plot_loops method from the visualize module—ideally with a different color from neo-loops on the heatmap to distinguish them.

Alternatively, if you’d like to focus specifically on the contact map within each neo-TAD, you could adjust the left and right boundary coordinates of each SV assembly to match the neo-TAD boundaries. In your example, the adjusted SV assembly would be:

A1 translocation,17,49985000,-,X,88215000,+ translocation,X,87885000,-,17,39305000,- 17,50120000 17,39400000

Xiaotao

[XiaoTaoWang]

By the way, I noticed that the contact frequencies between different fragments in your example appear disrupted and not very smooth. When constructing the Triangle object, you can manually adjust the overall interaction strength between regions using the slopes parameter. Each fragment pair should be assigned a value between 0 and 1, where a lower value corresponds to stronger interactions between the two corresponding fragments.

Please also refer to this issue #32 for more details.

[AuraStephenson]

Thank you I will adjust that.

Aura