How big are TAD boundaries?

Question

[annamariabugaj]

I have .bed files for TADs from experiments on neuronal fetal tissue downloaded from GEO (GSE77565). I need to extract the boundaries and I am not sure how long they should be. Is it ok to take 5kb flanks as you do for CCD boundaries?

Answer 1

[igor]

In Hi-C experiments, the boundary size is usually equal to the bin size.

The genome is split into bins. Each bin is assigned a boundary score. The bins with local maximum boundary scores become the boundaries and separate the neighboring TADs. Thus, each bin is either in a specific TAD or is a boundary.