搜索
查看: 3177|回复: 1

不同基因组版本坐标转换大全~biostar经典帖子

[复制链接]

634

主题

1182

帖子

4030

积分

管理员

Rank: 9Rank: 9Rank: 9

积分
4030
发表于 2017-1-12 22:18:31 | 显示全部楼层 |阅读模式
太经典了,值得学习:https://www.biostars.org/p/65558/
其实我博客也有好多介绍,你们想看中文也可以阅读。
liftover基因组版本直接的coordinate转换

基因组各种版本对应关系

用crossmap代替liftover做基因组坐标转换


There are at least three well known tools that can help you with these kinds of tasks:
  • UCSC liftOver. This tool is available through a simple web interface or it can be downloaded as a standalone executable. To use the executable you will also need to download the appropriate chain file. Each chain file describes conversions between a pair of genome assemblies. Liftover can be used through Galaxy as well. There is a python implementation of liftover called pyliftover that does conversion of point coordinates only.
  • NCBI Remap. This tool is conceptually similar to liftOver in that in manages conversions between a pair of genome assemblies but it uses different methods to achieve these mappings. It is also available through a simple web interface or you can use the API for NCBI Remap.
  • The Ensembl API. The final example I described above (converting between coordinate systems within a single genome assembly) can be accomplished with the Ensembl core API. Many examples are provided within the installation, overview, tutorial and documentation sections of the Ensembl API project. In particular, refer to these sections of the tutorial: 'Coordinates', 'Coordinate systems', 'Transform', and 'Transfer'. Ensembl also has a simple web service for coordinate conversions.
  • Bioconductor rtracklayer package. For R users, Bioconductor has an implementation of UCSC liftOver in the rtracklayer package. To see documentation on how to use it, open an R session and run the following commands.
  • CrossMap. A standalone open source program for convenient conversion of genome coordinates (or annotation files) between different assemblies. It supports most commonly used file formats including SAM/BAM, Wiggle/BigWig, BED, GFF/GTF, VCF. CrossMap is designed to liftover genome coordinates between assemblies. It’s not a program for aligning sequences to reference genome. Not recommended for converting genome coordinates between species.
    source("http://bioconductor.org/biocLite.R")
    biocLite("rtracklayer")
    library(rtracklayer)
    ?liftOver
  • Flo. A liftover pipeline for different reference genome builds of the same species. It describes the process as follows: "align the new assembly with the old one, process the alignment data to define how a coordinate or coordinate range on the old assembly should be transformed to the new assembly, transform the coordinates."


我比较希望用R来解决,所以我会试用一下,R里面的bioconductor系列包也可以进行坐标转换 http://www.bioconductor.org/help/workflows/liftOver/




上一篇:H3K27ac和H3K4me1两个组蛋白marker在ESC和NPC里面的变化区别?
下一篇:我想知道stella阳性细胞在干细胞领域研究作用!
你这个问题很复杂,需要打赏,请点击 http://www.bio-info-trainee.com/donate 进行打赏,谢谢
回复

使用道具 举报

634

主题

1182

帖子

4030

积分

管理员

Rank: 9Rank: 9Rank: 9

积分
4030
 楼主| 发表于 2017-1-12 22:23:02 | 显示全部楼层
  • UCSC liftover tool only supports BED input.
  • NCBI remap support BED, GFF, GTF, VCF, etc
  • Galaxy (Based on UCSC liftover tool) supports BED, GFF, GTF input.
  • Ensembl assembly converter supports BED, GFF, GTF, PSL input, but output is GFF only. (Update: The original “assembly converter” has been retired. Starting from 2015, Ensembl uses CrossMap to perform genome coordinate conversion.)
  • pyliftover “only does conversion of point coordinates, that is, unlike liftOver, it does not convert ranges, nor does it provide any special facilities to work with BED files”.

你这个问题很复杂,需要打赏,请点击 http://www.bio-info-trainee.com/donate 进行打赏,谢谢
回复 支持 反对

使用道具 举报

您需要登录后才可以回帖 登录 | 立即注册

本版积分规则

QQ|手机版|小黑屋|生信技能树 ( 粤ICP备15016384号  

GMT+8, 2019-9-22 00:13 , Processed in 0.028003 second(s), 25 queries .

Powered by Discuz! X3.2

© 2001-2013 Comsenz Inc.