Encoding zero-length features in BED format
What is the convention for encoding zero-length features (that is, features between two nucleotides) in BED format? Would I use [0, 0) or [1, 1) to describe the site between the 0th base and 1st base?
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Daniel Standage
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1,1 is the space between the 0th and 1st base in zero-based coordinates
0 1 2 3 4 zero-based coords
A C T G bases
1 2 3 4 one-based coords
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Chris Miller
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