TR region BED file - are start coordinates 1-based or 0-based?

[Ben Weisburd]

Would be nice to clarify this @ https://github.com/gymrek-lab/LongTR?tab=readme-ov-file#tr-region-bed-file

2. The start position of the TR on its chromosome

[Helia (Helyaneh) Ziaei Jam]

Hi Ben,

Start coordinates should be 1-based. I will add this to the documentation. Thank you!

Best,
Helia

[David Lougheed]

Hello,
It's worth noting that the UCSC and GA4GH BED specifications both require 0-based, half-open coordinates: https://genome.ucsc.edu/FAQ/FAQformat.html#format1 ; https://github.com/samtools/hts-specs/blob/master/BEDv1.pdf