pipeline questions: control sample and rerun skipping steps

[gianfilippo]

Hi,

I have a couple of questions about the pipeline. I am interested in CUT&RUN specifically, and do not have experience with it, yet

is there a way to specify the control samples, to be used together with target sample for peak calling ?

Also, in the usage section it says:
"Based on the results, users should select only one setting to go to steps 3 & 4."
How do I skip steps 1 and 2 and run only 3 and 4 ?

Thanks