ATAC-seq closed chromatin regions

Question

[rykerklie7]

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?

Thanks

[Friederike]

Can you define what you mean by "closed regions"?

ATAC-seq is a method for enriching regions of open chromatin, i.e. while you will still have the background sequences probably representing the bulk of the genome, the signal (= peaks) itself will always correspond to open chromatin (because those are the regions where the Tn5 transposase integrates and adds adapters for sequencing).

[rykerklie7]

I mean chromatin regions that are Inaccessible. Annotate chromatin regions as open (accessible) or closed (inaccessible).