Only one enzyme for 4c-seq analysis, How to analyze ?

Question

[htchd]

I have 4c-seq data from one enzyme experiment. But the pipelines I found use 2 enzymes for the analysis. Should I ignore 2nd enzyme or write the same enzyme in the configuration file?

[ATpoint]

If you used specialized software you cannot simply ignore or tweak parameters while expecting adequate results. These tools/workflows assume standard library protocols with two enzymes. Is this some special 4C-seq protocol? Why only one enzyme?

[htchd]

I'm using 4cseqpipe. The data gave to me is only one enzyme.