HI I have been following the ATACseq analysis galaxy training to analyze my ATACseq data. The tutorial is extremely user friendly and quite straight forward ( https://galaxyproject.github.io/training-material/topics/epigenetics/tutorials/atac-seq/tutorial.html), Thanks a lot for that. However, I have a concern about the step in between, or I seems to be overlooking it, I don’t seem to see a step of normalization to the read number?
In this tutorial, only one dataset is used to identify the chromatin regions. And there is no comparison between different samples (different cells).
For a current study about different normalization methods, see: https://epigeneticsandchromatin.biomedcentral.com/articles/10.1186/s13072-020-00342-y