UCSC 数据库提供了hg19和hg38位置转换工具---LiftOver
- 网页版:
https://genome.ucsc.edu/cgi-bin/hgLiftOver
图片.png
- 本地版:
(1)linux 环境下载Liftover
wget http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/liftOver
修改权限:
chmod 755 liftOver
(2)下载坐标注释文件:
<hg38ToHg19>
wget http://hgdownload.cse.ucsc.edu/goldenPath/hg38/liftOver/hg38ToHg19.over.chain.gz
<hg19ToHg38>
wget http://hgdownload.cse.ucsc.edu/goldenPath/hg19/liftOver/hg19ToHg38.over.chain.gz
(3)基本usage:
./liftOver <inbed> <over.chain.gz> <outputfile> <unmapedfile>
示例,hg19转hg38:
./liftOver test.bed hg19ToHg38.over.chain.gz test.map.bed test.unmap.bed
注意web 在线版和本地版对bed 文件格式不同:
web在线版:chr:start-end
本地版(3列,tab分隔): chr start end