Liftover是UCSC中用于基因组版本之间转换的一个工具,既可以做某一物种内基因组版本的转换,还可以做物种间基因组版本的转换。
1 网页转换
http://genome.ucsc.edu/cgi-bin/hgLiftOver
2. linux本地运行
### 下载软件
wget http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/liftOver
### 下载相关文件(hg38和hg19坐标转换)
wget http://hgdownload.cse.ucsc.edu/goldenPath/hg19/liftOver/hg19ToHg38.over.chain.gz
wget http://hgdownload.cse.ucsc.edu/goldenPath/hg38/liftOver/hg38ToHg19.over.chain.gz
### 执行转换
liftOver access-5k-mappable.hg19.bed hg19ToHg38.over.chain.gz access-5k-mappable.hg38.bed unMapped.txt
# access-5k-mappable.hg19.bed 需要转化的bed
# access-5k-mappable.hg38.bed 转化后的bed