Normalization Vectors with AddNorm (-w and -r)

[HengkuanLi]

Hello,
What exactly is the difference between the -w and -r in juicer_tools addNorm? After reading the official documentation, I'm still very confused. I would appreciate your help in clarifying this.
Many thanks!

[moshe-olshansky]

Hello,
Normally normalisation is done per chromosome (with -d option). With the -w flag the entire contact matrix (including inter-chromosomal contacts) is normalised.