How do I set "LIGATION_SITE" parameter for Dpn-II enzyme in the HiC-Pro config file ?

[medalofhonor]

I am working on a HiC dataset which was generated using the DpnII restriction enzyme. 

I was able to get the resfrag_hg19 bed file for DpnII using the digest_genome.py script, however, I am not sure what would be the correct sequence to set for the LIGATION_SITE parameter. 

DpnII's cut site is  5'--- ^GATC ---3' 

Thanks in advance. 

[nservant]

It should be GATCGATC
N

[Berkley Gryder]

My question too, thanks for answering!

[nservant]

Same answer ;)
Should be GATCGATC
However, note that it depends on the fill in strategy used to generate the libraries.
For instance, capture Hi-C protocols usually not include biotin fill in. In this case, the ligation motif is simply GATC.
Best