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.
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.