Why the scale of my Hi-C plot suddenly changed?

pyGenomeTracks is using HiCMatrix to read the matrix from h5 and cool format. From version 12 to version 13, a normalization step when reading cool file was removed. This normalization was mostly used when you were providing cool file from cooler balance.

If you want to keep the old scale you need to downgrade to HiCMatrix version 12 but version 13 also correct some bugs so we advice to change your max_value in your parameter file to adjust to the new scale.

No output generated with version 3.5 installed with pip

If you used pyGenomeTracks version 3.5 and the last line you get is:

INFO:pygenometracks.tracksClass:initialize x. [xxxxx]

It is highly probable that BEDTools is not installed or not loaded in your environment.

My Hi-C plot looks like no correction was applied when using cool matrix

pyGenomeTracks is using HiCMatrix to read the matrix from cool format. Unfortunately, a bug was introduced in version 14 ignoring the correction factors. This bug was fixed in version 15 so update HiCMatrix to last version should fix it.