Tassel 5.0关联分析软件 中文使用手册

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目录
引言 .................................................................................................................................................. 6 1 入门指南....................................................................................................................................... 7 1.1 执行 TASSEL .................................................................................................................... 8 1.2 开源代码............................................................................................................................ 8 1.3 软件开发工具.................................................................................................................... 8 1.4 图形界面............................................................................................................................ 9 1.5 管道（命令行界面） ...................................................................................................... 10 1.6 GBS 管道 .......................................................................................................................... 10 2 File（文件）菜单 ....................................................................................................................... 10 2.1.1 Save Data Tree（保存数据树） ............................................................................ 10 2.1.2 Open Data Tree（打开数据树）............................................................................ 10 2.1.3 Save Data Tree As…（数据树另存为…） ........................................................... 10 2.1.4 Open Data Tree…（打开数据树…）.................................................................... 11 2.1.5 Set Preferences（设置首选项） ............................................................................ 11 3 Data（数据）菜单 ................................................................................................................. 11 3.1 Load（加载） .................................................................................................................. 12 3.1.1 Hapmap ........................................................................................................... 14 3.1.2 3.1.3 3.1.4 HDF5（层次数据格式，版本５） ............................................................... 14 VCF（Variant Call Format 变异体召唤格式） ............................................ 15 Plink ................................................................................................................ 15
Contributors: Ed Buckler, Terry Casstevens, Peter Bradbury, Zhiwu Zhang, Dallas Kroon, Jeff Glaubitz, Kelly Swarts, Jason Wallace, Fei Lu, Alberto Romero, Cinta Romay, Eli Rodgers-Melnick, Alexander Lipka, Sara Miller, James Harriman, Yogesh Ramdoss, Michael Oak, Karin Holmberg, Natalie Stevens, and Yang Zhang.
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TASSEL 项目由国家科学基金和 USDA-ARS 资助
Βιβλιοθήκη Baidu
相关的链接：
主网站：http://www.maizegenetics.net/tassel 开源代码：https://bitbucket.org/tasseladmin/tassel-5-source Wiki：https://bitbucket.org/tasseladmin/tassel-5-source/wiki
TASSEL5.0 用户手册
Cornell 大学 Buckler 实验室
(June 12, 2014)
翻译：陈建国 湖北大学生命科学学院
www.maizegenetics.net/tassel
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声明：虽然 Cornell 大学 Buckler 实验室已经进行了广泛的测试并且一般来说结果是可靠的、 正确的或合适的， 但是对于任何一套特定的数据不能保证一定能够得到你想要的结果。 强烈 地建议用户利用其它软件来验证 TASSEL 的结果。
3.1.5 投影校准（Projection Alignment）............................................................... 15 3.1.6 Phylip .............................................................................................................. 15 3.1.7 FASTA............................................................................................................. 16 3.1.8 Numerical Data（数值数据） ....................................................................... 16 3.1.9 Square Numerical Matrix（数值方阵） ........................................................ 17 3.1.10 Table Report（表格报告） .......................................................................... 18 3.1.11 TOPM（Tags on Physical Map，物理图谱上的标签）............................... 18 3.2 Export 导出 ....................................................................................................................... 18 3.3 转换（Transform） ......................................................................................................... 19 3.3.1 Genotype Numericalization（基因型数字化） .................................................... 19 3.3.2 Transform and/or Standardize Data 转换和/或标准化数据.................................. 20 3.3.3 Impute Phenotype 估算表现型.............................................................................. 21 3.3.4 PCA（主成分分析） ............................................................................................ 22 3.4 Synonymizer（举出分类单元名称的同义词）...................................................... 23 3.5 Intersect Join（交集合并） ............................................................................................. 25 3.6 Union Join（并集合并） ................................................................................................. 26 3.7 Merge Genotype Tables（合并基因型表格）................................................................. 26 3.8 Separate（分离） ............................................................................................................. 27 3.9 Homozygous Genotype（纯合的基因型） ..................................................................... 27 4 Impute（估算）菜单 .................................................................................................................. 27 5 Filter（过滤）菜单 ..................................................................................................................... 35 5.1 Sites（位点） ................................................................................................................... 35
Citations: Overall Package: Bradbury PJ, Zhang Z, Kroon DE, Casstevens TM, Ramdoss Y, Buckler ES. (2007) TASSEL: Software for association mapping of complex traits in diverse samples. Bioinformatics 23:2633-2635. Genotyping by Sequencing: Glaubitz JC, Casstevens TM, Lu F, Harriman J, Elshire RJ, Sun Q, Buckler ES. (2014) TASSELGBS: A High Capacity Genotyping by Sequencing Analysis Pipeline. PLoS ONE 9(2): e90346 Mixed Model GWAS: Zhang Z, Ersoz E, Lai C-Q, Todhunter RJ, Tiwari HK, Gore MA, Bradbury PJ, Yu J, Arnett DK, Ordovas JM, Buckler ES. (2010) Mixed linear model approach adapted for genome-wide association studies. Nature Genetics 42:355-360.
更多的帮助：除了这个文档以外还可以得到额外的帮助。欢迎用户报告软件的缺陷，通过 TASSEL 网址申请新的性能。也欢迎对我们现在的团队成员提出问题。要想得到更快速和更 准确的答案，请把你的问题提交给最相关的人： Tassel 用户群（推荐） 一般的信息 数据输入，Pipeline 统计分析 http://groups.google.com/group/tassel tassel@googlegroups.com Ed Buckler（项目领导人） esb33@cornell.edu Terry Casstevens tmc46@cornell.edu Peter Bradbury pjb39@cornell.edu