How to define short- and long-range interactions in this tool

[hanshanmengqi]

Hello developer:

Sorry to disturb you & thank you for this amazing tool.

Now I have question about how to define short- and long-range interactions? Because I'm work on plant not animal and probably I need use different parameters for analysis Hi‑C data.

Best,
Han

[magnitov]

Hi Han,

These are actually determined automatically based on compartments you provide. The short-range are those residing on diagonal, while long-range are those off-diagonal. Simply, the script finds stretches of compartments A and B and their intersects. The diagonal bits are becoming short-range, and their off-diagonal pairwise intersections are long-range. Please check Figure 1 in the original paper or supplemented illustrations on Github.

Mikhail