I would like your advice about normalization with cn.MOPs - as I understand cn.MOPs algorithm includes normalization to compare between different loci and across different samples. cn.MOPs also contains the "normalize genome" function to compare across samples. What is the difference between these two options? I am working with a dataset of variable read depth samples ranging from 7x to 51x with an average of 16x. What is your recommendation for normalizing across these different samples? Should the "normalize genome" option be used?
Thank you for your help.