FAQ¶
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.