Hello, I am analysing ChIP-seq data and I saw the following post by @Devon Ryan (made 1 year, 7 months ago) https://bioinformatics.stackexchange.com/questions/458/when-to-account-for-the-blacklisted-genomic-regions-in-chip-seq-data-analyses/459#459?newreg=dca76bad61c443d7b4f0b1abd1487878 saying that, nowadays with the latest genome assemblies, one has less problems with blacklisted regions since they have been reduced.
I want to know, then, what's the state of the art of this situation? Should I remove them or not? (By the way, I was planning to use Deeptools to do it, but if it's not really necessary anymore I won't). Thank you!