Q: how do slocal amd llocal work with open/closed chromatin domains?

[linpei26]

Hello everyone,

I found this text from MACS2 document

By default, MACS considers 1000bp for small local region(--slocal), and 10000bps for large local region(--llocal) which captures the bias from a long-range effect like an open chromatin domain.

Could anyone please help provide some more explanation?

I guess that this means that if an open chromatin domain was encountered, it would be better for MACS2 to compute a local lambda by scanning a larger local region, rather than a small one. If not an open chromatin, scanning a small local region should be good enough.

Am I right?

However, I feel that at the whole genome scale, one may find some regions within open chromatin domain while other regions not. But peaks could be found in both types of regions. How does MACS2 determine whether small or large local region should be invoked?

Thanks!