Ambiguous site handling hicBuildMatrix --restrictionSequence --danglingSequence

[TheGreatJack]

Hello

I havent found clear documentation on the topic of hicBuildMatrix handling ambiguous IUPAC bases. I'm working on data made with the Arima kit which it seems to use the enzymes DnpII and HinfI. DnpII is fine with "GATC" for site and dangling sequence but HinfI uses "GANTC" with dangling sequence "ANT". It is not clear if i can use the following parameters without problems:

"--restrictionSequence GATC GANTC --danglingSequence GATC ANT"

Or if i have to manually expand the site for HinfI as if i had 4 enzymes "GAATC","GATTC","GAGTC" and "GACTC". My worry also stems from the fact that "hicFindRestSite 3.7.6", wasnt able to parse "GANTC", and returned an emtpy bed file. It only returned data when i used "GA.TC" as it uses regex under the hood.

I'm using hicExplorer v3.7.6 downloaded from conda.

I wasnt able to find info related to this specific topic, though the arima kit has been mentioned before.

Any insight is appreciated, thank you