I am analysing ChIA-PET data using ChIA-PET2 tool. I wanted to know what exactly the following terms mean from the trim statistics the tool provides:
Expect PETs Expect both PETs 1Empty PETs 2Empty PETs Valid PETs
What is the difference between Expected and Expected both PETs? And similarly what exactly does 1 Empty and 2 Empty mean? Is it related to absence of the linker sequences in the reads? Also, how does the tool detect which PETs are valid? None of the information is provided in the tool paper. Any help would be appreciated. Thanks!