I launched an analysis of some ATACseq data across different conditions. I launch the cf-core ATACseq pipeline v 1.2.1:
In the output I have a PCA generated by DESeq2 from read normalized. The exact sentence is :
"The script included in the pipeline uses DESeq2 to normalise read counts across all of the provided samples in order to create a PCA plot and a clustered heatmap showing pairwise Euclidean distances between the samples in the experiment"
My question is the following: What is the number of counts per accessible region across replicates used for this PCA ? All reads, only the 500 most variable accessible regions ? I think it is the lastest but can't find the explicit information and now I am wondering.
Thank you in advance for your response !