ASSEL - CGIARhpc.ilri.cgiar.org/beca/training/NaroBFX2014/course/Tassel_how_to.p… · Write BLOB...
Transcript of ASSEL - CGIARhpc.ilri.cgiar.org/beca/training/NaroBFX2014/course/Tassel_how_to.p… · Write BLOB...
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TASSEL
Trait�Analysis�by�aSSociation,�Evolution�and�Linkage
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Getting�TASSEL
• www.maizegenetics.net/tassel• Java�application�that�runs�on�your�computer• launch�from�the�website�(tassel3.jnlp)– downloads�TASSEL�and�library�files�once– checks�for�latest�version�after�that
• download�standalone– run�without�a�web�connection– increase�available�memory
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Edit�the�start_tassel.bat�file�in�tassel3.0_standalone�to�increase�the�available�memory
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Documentation
• User’s�Guide• Tutorial– Part�of�users�guide– Tutorial�data�set
• Pipeline– Allows�TASSEL�to�be�run�from�the�command�line
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Resources
To�report�problems�or�make�feature�requests
To�ask�questions�about�TASSEL�use
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General�OrganizationMain�Function�Categories
Data�sets�and�reports�– stored�in�RAM
Comments�about�data�and�reports
Task�progress
Tasks�specific�to�main�category
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Import�Formats
• Hapmap• Plink• Flapjack• Polymorphism• Phylip• Numerical�Data�(traits�or�markers)• Square�Numerical�Matrix�(kinship)• Genetic�Map• Guess�function
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Exporting�Data
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Downloading�Data�From�the�HordeumToolbox
• http://hordeumtoolbox.org/• now�http://triticeaetoolbox.org/
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I�will�make�my�best�guess�and�try
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Load�Flapjack
Genetic�positions�mutliplied by�1000
Flapjack�import�options
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Original�data�set
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Running�Linkage�Disequilibrium�Analysis
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Display��an�LD�Plot
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Steps�for�running�PCA�analysis
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With�multiple�location�data,�GLM�or�MLM�will�be�faster�if�entry�means�are�calculated�first�using�GLM�for�BLUEs�or�other�software�for�calculating�BLUPs
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Join�the�resulting�data�set�with�marker�and,�optionally,�population�structure�covariates
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Option�for�saving�output�to�disk�for�large�files
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R�Package�for�Association�Analysis�and�Genomic�Selection
visit�http://www.maizegenetics.net/gapit�or�just�google GAPIT