I have chromatin data, from ATAC and other histone marks and RNA-Seq data for same samples. Lets say I have 14 independent samples subjected to ATAC-Seq and RNA-Seq, but at different times, different sequencing centres.
Now I want to compare the signal from chromatin data to gene expression data, lets say calculating the correlation values of chromatin signal at a peak to near by gene expression levels.
As this data is not directly comparable to each other, and sequencing depth normalisation is not enough, I would like to know how to make this data sets comparable to each other such that the analysis is biologically valid and accepted for publication. I could not find any online methods for this sort of analysis, though its been shown in many papers.