Tassel-5.0关联分析软件-中文使用手册

TASSEL5.0用户手册Cornell大学Buckler实验室(June12,2014)翻译：陈建国湖北大学生命科学学院声明：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。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）@googlegroups.com一般的信息EdBuckler（项目领导人）[e-mail]数据输入，[e-mail]统计分析[e-mail]:EdBuckler,TerryCasstevens,PeterBradbury,ZhiwuZhang,DallasKroon,JeffGlaubitz,KellySwarts,JasonWallace,FeiLu,AlbertoRomero,CintaRomay,EliRodgers-Melnick,AlexanderLipka,SaraMiller,JamesHarriman,YogeshRamdoss,MichaelOak,KarinHolmberg,NatalieStevens,andYangZhang.Citations:OverallPackage:BradburyPJ,ZhangZ,KroonDE,CasstevensTM,RamdossY,BucklerES.(2007)TASSEL:Softwareforassociationmappingofcomplextraitsindiversesamples.Bioinformatics23:2633-2635.GenotypingbySequencing:GlaubitzJC,CasstevensTM,LuF,HarrimanJ,ElshireRJ,SunQ,BucklerES.(2014)TASSEL-GBS:AHighCapacityGenotypingbySequencingAnalysisPipeline.PLoSONE9(2):e90346MixedModelGWAS:ZhangZ,ErsozE,LaiC-Q,TodhunterRJ,TiwariHK,GoreMA,BradburyPJ,YuJ,ArnettDK,OrdovasJM,BucklerES.(2010)Mixedlinearmodelapproachadaptedforgenome-wideassociationstudies.NatureGenetics42:355-360.2TASSEL项目由国家科学基金和USDA-ARS资助相关的链接：主网站：开源代码：：目录引言..................................................................................................................................................61入门指南.......................................................................................................................................71.1执行TASSEL....................................................................................................................81.2开源代码............................................................................................................................81.3软件开发工具....................................................................................................................81.4图形界面............................................................................................................................91.5管道（命令行界面）......................................................................................................101.6GBS管道..........................................................................................................................102File（文件）菜单.......................................................................................................................102.1.1SaveDataTree（保存数据树）............................................................................102.1.2OpenDataTree（打开数据树）............................................................................102.1.3SaveDataTreeAs…（数据树另存为…）...........................................................102.1.4OpenDataTree…（打开数据树…）....................................................................112.1.5SetPreferences（设置首选项）............................................................................113Data（数据）菜单.................................................................................................................113.1Load（加载）..................................................................................................................123.1.1Hapmap...........................................................................................................143.1.2HDF5（层次数据格式，版本５）...............................................................143.1.3VCF（VariantCallFormat变异体召唤格式）............................................153.1.4Plink................................................................................................................153.1.5投影校准（ProjectionAlignment）...............................................................153.1.6Phylip..............................................................................................................153.1.7FASTA.............................................................................................................163.1.8NumericalData（数值数据）.......................................................................163.1.9SquareNumericalMatrix（数值方阵）........................................................173.1.10TableReport（表格报告）..........................................................................183.1.11TOPM（TagsonPhysicalMap，物理图谱上的标签）...............................183.2Export导出.......................................................................................................................183.3转换（Transform）.........................................................................................................193.3.1GenotypeNumericalization（基因型数字化）....................................................193.3.2Transformand/orStandardizeData转换和/或标准化数据..................................203.3.3ImputePhenotype