TR region BED file - are start coordinates 1-based or 0-based?
bw2 opened this issue · comments
Ben Weisburd commented
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 commented
Hi Ben,
Start coordinates should be 1-based. I will add this to the documentation. Thank you!
Best,
Helia
David Lougheed commented
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