Inconsistency between the defenition of the BED format according to UCSC and bedtools.

[Daniel Ariad]

It seems that the description of the the BED format in the webpages of UCSC browser(https://bedtools.readthedocs.io/en/latest/content/general-usage.html) and BEDtools(https://bedtools.readthedocs.io/en/latest/content/general-usage.html) are inconsistent;

bedtools: For example, start=9, end=20 is interpreted to span bases 10 through 20,inclusive.

UCSC browser: For example, the first 100 bases of chromosome 1 are defined as chrom=1, chromStart=0, chromEnd=100, and span the bases numbered 0-99 in our software (not 0-100), but will represent the position notation chr1:1-100.

Does anyone understand why the two definitions of the BED format are inconsistent ???

[Aaron Quinlan]

Hi Daniel,

This is indeed confusing. UCSC uses the same convention as bedtools to represent intervals, but it converts to closed, inclusive intervakls when displaying things on the browser. To make things more confusing, I feel that this statement "and span the bases numbered 0-99 in our software” is wrong - they mean the first through the hundredth nucleotides. 

I always find this reference helpful:  https://www.biostars.org/p/84686/

Best,

Aaron

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