【3.1】One-Based和Zero-Based区别

用bedtools等工具的时候，就已经困惑了，为什么有的文件是0-based的，有的是1-based。直到前几天，zh发给我了一个连接，才彻底释怀。

In addition to the illustrations/explanation below, Ben Ainscough (a member of our lab) has created a python tool to convert between zero and one based coordinate systems here: https://github.com/griffithlab/convert_zero_one_based

一 0-based和1-based的区别

• 1-based coordinate system
  Numbers nucleotides directly
• 0-based coordinate system
  Numbers between nucleotides

二 0-based和1-based都有哪些应用

Ensembl uses 1-based coordinate system UCSC uses 0-based coordinate system

1-based (GFF, SAM, VCF，BLAST))
0-based (BED, BAM，)

三 0-based和1-based的转换

0-based coordinates to 1-based

if (type=SNV){start=start+1; end=end;}
if (type=DEL){start=start+1; end=end;}
if (type=INS){start=start; end=end+1;}

1-based coordinates to 0-based

if (type=SNV){start=start-1; end=end;}
if (type=DEL){start=start-1; end=end;}
if (type=INS){start=start; end=end-1;}

资料

• https://www.biostars.org/p/84686/
• https://www.biostars.org/p/6373/