进入http://hgdownload.soe.ucsc.edu/admin/exe/下载页面,根据自己的系统选择对应版本的工具文件进行下载,这里以linux.x86_64的版本为例。 同时,根据下面的链接,按照不同基因组版本下载转换需要的map.chain注释文件https://hgdownload.soe.ucsc.edu/goldenPath/hg19/liftOver/hg19ToHg38.over.chain.gz https://hg...
进入http://hgdownload.soe.ucsc.edu/admin/exe/下载页面,根据自己的系统选择对应版本的工具文件进行下载,这里以linux.x86_64的版本为例。 同时,根据下面的链接,按照不同基因组版本下载转换需要的map.chain注释文件https://hgdownload.soe.ucsc.edu/goldenPath/hg19/liftOver/hg19ToHg38.over.chain.gz https://hg...
chomd +x ./liftover #更改下载的liftover的执行权限 wget http://hgdownload.soe.ucsc.edu/goldenPath/hg19/liftOver/hg19ToHg38.over.chain.gz #下载从hg19到hg38版转换的注释文件,其他的注释文件可以在http://hgdownload.soe.ucsc.edu/downloads.html#human中的LiftOver files下载 liftover使用 1.将liftOver变...
2 下载坐标转换对应文件,hg38TOhg19 wget http://hgdownload.soe.ucsc.edu/goldenPath/hg38/liftOver/hg38ToHg19.over.chain.gz gunzip hg38ToHg19.over.chain.gz 3 下载转换工具 wget-c http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/liftOver chmod755liftOver./liftOver 4 进行转换 ./liftOver...
今天用liftover做基因组转换的时候,hg38转hg19,所有的位点都转失败了。看到提示为“#Deleted in new”。一般这个错误为是由于hg19 (要转换的基因组) 中没有该区域导致的。但是这么多位点都没有,估计是提供的文件有问题了。 检查了一下,发现给的bed文件是这样的: ...
(3) download chain file http://hgdownload.cse.ucsc.edu/goldenpath/hg19/liftOver/ (4) prepare input bed file (chr start end others ...) (5) run liftOver ./liftOver input.bed hg18ToHg19.over.chain.gz output.bed unlifted.bed 1. ...
(3) download chain filehttp://hgdownload.cse.ucsc.edu/goldenpath/hg19/liftOver/ (4) prepare input bed file (chr start end others ...) (5) run liftOver ./liftOver input.bed hg18ToHg19.over.chain.gz output.bed unlifted.bed unlifted.bed file will contain all genome positions that cannot...
(3) download chain filehttp://hgdownload.cse.ucsc.edu/goldenpath/hg19/liftOver/ (4) prepare input bed file (chr start end others ...) (5) run liftOver ./liftOver input.bed hg18ToHg19.over.chain.gz output.bed unlifted.bed unlifted.bed file will contain all genome positions that cannot...
用liftover软件 # Download liftOver tool (replace with the appropriate URL for your OS) wget http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/liftOver # Make it executable chmod +x liftOver # Do…
segment_liftover -l ./liftOver -i /Volumes/data/hg18/ -o /Volumes/data/hg19/ -c hg18ToHg19 -si segments.tsv -so seg.tsv Demo mode segment_liftover -l .liftOver --demo . This will copy a few example files to the current directory and run a quick conversion with default settings. ...