I am looking to extract both open and closed chromatin regions from ATAC-seq data. Could the mapped sequenced reads <130bp be identified as open chromatin regions? So what constitutes the closed chromatin regions.
I would like to call peaks from open chromatin/nucleosome-free regions, and after annotating look for specific genes that fall into this category. Similarly, I would like to call for peaks in closed chromatin regions.
How do I go about identifying the closed regions from mapped sequenced reads?