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biocore-ntnu / epic2

Ultraperformant reimplementation of SICER
https://doi.org/10.1093/bioinformatics/btz232
MIT License
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Are output coordinates one or zero-based? #55

Open rauldiul opened 2 years ago

rauldiul commented 2 years ago

Hi!

Thank you for your work!!

I have a simple question: the epic2 output comes in BED-similar format, however, I'm not sure if the output is really 0-based. When I do peak calling, if I check the minimum peak size obtained (which should be equal to the --bin-size argument), by doing End - Start, I get 1 bp less than --bin-size.

E.g. when peak calling with default parameters, the minimum peak size I observe is 199 bp. Thus, to get 200 bp, I would have to do End - Start + 1, which is compatible with the output being 1-based instead of 0-based.

Could you confirm this?

thanks for your help!

endrebak commented 2 years ago

I just followed what SICER did. 0-199, 200-499 etc. This means that the start is 0-based and the end is 1-based

endrebak commented 2 years ago

:)

rauldiul commented 2 years ago

Thanks for the response! But then (and sorry for the misguided/ignorant question), does that mean that the window sizes are actually 199 bp wide? I was trying to compare them to the UCSC coordinate systems where 0-start + 1-end means the end coordinate is excluded from the intervals. But maybe the meaning here is different or I am (probably) confused.