This is a basic question, but I haven't seen the answer anywhere. In the BED format, how are the nucleotides numbered on the sense and antisense strand. Does nt 1 on the sense strand bind with nt 1 on the antisense strand? Or is the last numbered nucleotide on the antisense strand the one to which nt 1 on the sense strand binds?
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written
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KCC
2 answers
I think you might want to read the description of the BED format
Strandedness is related to features and designated + and - per feature
Chromosomes start at base 0, and are defined by your reference genome.
There is no separate numbering scheme for sense/antisense bases.
As Daniel says, sense and antisense features have the same numbering system in the BED format, it is the strand column (number 6) that determines whether a feature is sense or antisense. However it is not strictly true that BED format requires a zero-based numbering system (e.g. like MAF), although this is what is in fact used by UCSC. The coordinate system is separately defined from the file format
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