how to generate merged_nodups.txt using juicer for omni-c seq reads

[Pramod Pantha]

Hi, I’m trying to use 3D-DNA for scaffolding the draft genome using omni -c seq reads. How do we generate merged_nodups.txt file using juicer? generate_site_positions.py requires restriction enzyme and must be one of ['HindIII', 'DpnII', 'MboI', 'Sau3AI', 'Arima']. I could not find a way to use DNASE there. Is there anything I’m missing here? Any help provided will be greatly appreciated.

Thanks

[Moshe Olshansky]

Hi there,

For DNASE you should specify "none", i.e. no restriction enzyme.