How are DNAse-seq data processed with this pipeline?

[Suffi Azizan]

I read the README and it was briefly mentioned that one can use the switch dnase instead of atac to use this pipeline with single-end DNAse-seq data. A test run I did yesterday with my own data completed successfully, but a quick look at the croo-generated html seems to suggest that dnase sequencing reads are processed pretty much similarly to atac-seq. I do not have much experience in DNAse-seq so far, so I need some clarification when using this pipeline with DNAse-seq sequencing data.

1. Is Dnase-I bias cleavage bias correction done when setting the option dnase in the pipeline input JSON?
2. My assumption is the macs2 was run with the parameters optimized for Dnase-seq data? So the output peak files can directly be used for downstream analysis to infer 'Dnase hypersensitive regions' == accessible chromatin regions?