Hi, everyone!

Sorry for all the questions. I try my best to search for the answers myself, but a lot of threads I find aren't very up-to-date. This is a follow-up question to something I posted a few days ago here.

My question this time is mostly related to industry best practices when it comes to ChIP-seq and RNA-seq count normalization. Let's say you're comparing data from two different studies but you're re-processing all the raw data from scratch to avoid any differences stemming from data treatment.

I was thinking the process would go something like: mapping --> normalizing against input --> comparison through a PCA

So my questions are:

1. What is the current industry standard for normalizing sequencing depth?
2. Which tools do you use for normalizing against input? Or do most people only do that once it's time to start peak calling?

Thank you! Here's a picture of a sea otter striking a power pose as thanks for reading through my post!