Half-Open And Closed Experiment Notation In Chip-Seq

Question

[Sukhi Singh]

Hi, I was using 'pyicos' a tool for NGS , I came across the notation of half-open and closed. what does it signifies, is it something to do with bed file notation (I think so) or ChIP-Seq itself.

From the pyicos callpeaks -h

optional arguments: -h, --help show this help message and exit

-o, --open-experiment Defines if the experiment is half-open or closed notation. [Default False]

Answer 1

[Vikas Bansal]

Half open and close are related to coordinates. Half open is zero based, meaning the first base on a chromosome is numbered 0. You can find more details here and biostar discussion here.

[Sukhi Singh]

Thanks Vikas!!!