Chromosome Coordinates On The Sense And Antisense Strands In The Bed Format

Question

[KCC]

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?

Answer 1

[User 59]

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.

[KCC]

So, just to be clear, the answer is nt 0 on the sense strand (or to be more precise, the first nucleotide indicated in the feature "chr1 0 100 a1 1 +") would be the one that binds to nt 0 on the antisense strand. Is this right?

Answer 2

[Casey Bergman]

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

[User 59]

Thanks Casey, you are of course correct that's the UCSC numbering convention.