Can chromosight detect loops based on restriction fragments level (1f, 2f, etc) HI-C matrix.

[koszullab]

Can chromosight detect loops based on restriction fragments level (1f, 2f, etc) HI-C matrix.

[cmdoret]

Hi @Linhua-Sun,

Unfortunately, this is not feasible with chromosight CLI. We rely on uniform bin sizes at several places to speed up algorithms. For example, the matrix is trimmed to the Nth diagonal based on max_-dist, if bins had different size, we could not establish a constant relationship between a distance and number of pixels.

It is possible to use chromosight's API in a python script to do this, but would require some additional work. The way to do this would be to provide the sparse contact matrix and loop kernel directly to normxcorr2 to compute the convolution (i.e. loop-similarity) matrix,feed this matrix to pick_foci to segment loops and retrieve the list of foci (loops) coordinates in rows/cols. validate_patterns and remove_neighbours could also help for filtering those patterns afterwards.

[Linhua-Sun]

Thank you very much for your prompt reply, which answered my question very well！