hayidahubei的个人博客分享 http://blog.sciencenet.cn/u/hayidahubei

博文

利用liftOver进行不同版本的坐标转换

已有 4412 次阅读 2018-12-15 10:43 |个人分类:基因组注释信息|系统分类:科研笔记| lift, over

Here I want to show how to convert coordinates from mm10 to mm9 based on command line. 

And you also can do this using the web interface at http://genome.ucsc.edu/cgi-bin/hgLiftOver

 

The operating system in my computer is Ubuntu 18.10 (64-bit).

 

Liftover usage:

liftOver input.bed map.chain output.bed unlifted.bed

 

You need download two files from UCSC. The first one is liftOver, and the second one is ”map.chain”.


You can download liftOver from http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/, and download ”map.chain”( mm10ToMm9.over.chain.gz) from http://hgdownload.cse.ucsc.edu/goldenPath/mm10/liftOver/.


Then you can use the code listed above to convert the coordinate from mm10 to mm9


The code I used is showed below:


liftOver ./ElementFromGtf/gene.bed /media/chunjie/hd2/Software/liftOver/mm10ToMm9.over.chain ./ElementToMM9/gene.bed ./ElementToMM9/unlifted.gene.bed




https://blog.sciencenet.cn/blog-1113671-1151651.html

上一篇:[转载]CDS, Exon, intron, utr的定义
下一篇:Ensembl/Gencode数据库中基因注释统计
收藏 IP: 130.91.194.*| 热度|

0

该博文允许注册用户评论 请点击登录 评论 (0 个评论)

数据加载中...

Archiver|手机版|科学网 ( 京ICP备07017567号-12 )

GMT+8, 2023-9-30 03:39

Powered by ScienceNet.cn

Copyright © 2007- 中国科学报社

返回顶部