Combined ENCODE DNase-Seq and ATAC-Seq PCA analysis – normalization across datasets – clustering example of human coronary artery smooth muscle cells.

Here I describe an approach using principal component analysis to cluster ATAC-Seq data onto ENCODE DNase-Seq data sets, in total 125 data sets, in order to distinguish data sets based on open chromatin signal intensity. I describe necessary steps in data filtering and data normalization to best calculate principal component analysis. I show an example of external human coronary artery smooth muscle cells ATAC-Seq data set clustering near human aortic smooth muscle cell DNase-Seq set from ENCODE.