What should I do after peak calling?

[FionaMoon]

Hi eCLIP group,
Thank you for sharing your pipline. I'm a little bit confused about what to do with next step after clipper peak calling.
In the documentary eCLIP_analysisSOP_pipeline.pdf, we should do 'Input normalization' like this:

However, after this, the next charpter is Peak normalization vs SMInput and reproducible peak / IDR analysis. This step uses merge_peaks pipline.

I wonder if input normalization equals to Peak normalization ?

I have 3 samples (2 replicates from patients,1 from healthy control), 2 reps have been merged in Samtools merge (PE only) step.
After peak calling, what should I do to normalize and make comparsion of my samples?

Thank you in advance!