Mapping without RE

[Pavla Navratilova]

Hi, I am using the Arima kit and their restriction enzyme cocktail for HiC. I tested the analysis with and without RE specification (leaving the 'GENOME_FRAGMENT =' and 'LIGATION_SITE =' blank. I am puzzled by finding that the mapping rate decreased from 71 to 51% and eventually, I got only half the number of valid pairs compared to the analysis with RE.

Does anyone have an idea what is going on? Is it wiser to add NNNNN as an extra RE to increase the number of valid pairs by covering the star activity of the other enzymes?

Thank you for your suggestions,

Pavla