TASSEL - Trait Analysis by Association, Evolution and Linkage

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WELCOME to TASSEL!

Welcome to the TASSEL-software forum. This discussion group provides an online source of information about the program TASSEL, for Association Mapping. The software and further information, as well as links to the original publications, can be found at the Buckler Lab for Maize Genetics and Diversity website, http://www.maizegenetics.net. R front-end for TASSEL (rtassel) is at https://bitbucket.org/bucklerlab/rtassel/src/master/

TASSEL is a software package to evaluate genotype and traits associations with the tools of population and quantitative genetics. TASSEL can handle datasets with commonly encountered in the plant community, e.g. replicated trials, inbred lines, and complex structured pedigrees. TASSEL also has the latest and statistically most powerful approaches for association mapping in complex populations [both General Linear Model (GLM) and Mixed Linear Model (MLM)]. In the latest version, speed and memory efficiency have been important foci so that it can now handle millions of SNPs and conduct powerful tests with them much more rapidly than general purpose analysis packages.

TASSEL is an Open Source software, and can be found at https://bitbucket.org/tasseladmin/tassel-5-source/wiki/Home

TASSEL user manual is available online at https://bitbucket.org/tasseladmin/tassel-5-source/wiki/UserManual. Additional help is available beyond this document. Users are welcome to report bugs, request new features through the TASSEL website.

A visual tutorial is available at https://www.youtube.com/channel/UCS1SdXlyMI1OsSf5yA_oFqw

We recommend searching the archives first before posting questions on the discussion group...

Please try to use informative subject lines for queries/comments! For bug reports please include as much information as possible including any error messages, the operating system, TASSEL version number, and whether you are using the stand-alone or web interface.

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Vasileia Spyridaki, Terry Casstevens3

Oct 3

Tassel pipeline - LinkageDisequilibriumPlugin

Thank you very much, Terry. It worked! Cheers. Στις Τετάρτη 2 Οκτωβρίου 2024 στις 11:58:12 μ.μ. UTC+8

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Tassel pipeline - LinkageDisequilibriumPlugin

Thank you very much, Terry. It worked! Cheers. Στις Τετάρτη 2 Οκτωβρίου 2024 στις 11:58:12 μ.μ. UTC+8

Oct 3

Umer Nb, Terry Casstevens2

Sep 5

File uploading issue

Did you check SNP ss715578788? H is not a possible allele value? On Thu, Sep 5, 2024 at 5:33 PM Umer

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File uploading issue

Did you check SNP ss715578788? H is not a possible allele value? On Thu, Sep 5, 2024 at 5:33 PM Umer

Sep 5

Hrithik Mangla L- A26

Aug 20

Stepwise Regression Plugin

Hii everyone, I am using Stepwise plugin in TASSEL GUI v5 for QTL mapping of the traits in BC1F2

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Stepwise Regression Plugin

Hii everyone, I am using Stepwise plugin in TASSEL GUI v5 for QTL mapping of the traits in BC1F2

Aug 20

Terry Casstevens

Aug 20

Tassel 5.2.94 / PHG 1.10 Build

I've posted the latest build for Tassel 5 including PHG 1.10 to the web site. This release fixes

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Tassel 5.2.94 / PHG 1.10 Build

I've posted the latest build for Tassel 5 including PHG 1.10 to the web site. This release fixes

Aug 20

Celia VI, … Terry Casstevens3

Jul 29

Number of SNPs altered

You are using a really old update of TASSEL 5. Please update to the latest version. https://bitbucket

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Number of SNPs altered

You are using a really old update of TASSEL 5. Please update to the latest version. https://bitbucket

Jul 29

FATIMA IGUENFAR, Terry Casstevens2

Jul 23

Assistance Required for TASSEL Genotypic Data Error

Please follow these instructions to get more information. https://bitbucket.org/tasseladmin/tassel-5-

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Assistance Required for TASSEL Genotypic Data Error

Please follow these instructions to get more information. https://bitbucket.org/tasseladmin/tassel-5-

Jul 23

Niranjan Mahadevan, Terry Casstevens3

Jul 14

hapmap data import error

Dear Terry Thanks a lot. It worked On Monday, July 15, 2024 at 11:01:30 AM UTC+9 Terry Casstevens

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hapmap data import error

Dear Terry Thanks a lot. It worked On Monday, July 15, 2024 at 11:01:30 AM UTC+9 Terry Casstevens

Jul 14

Jul 3

Structure Analysis

Hello everyone, I will perform a STRUCTURE analysis for the SNP marker file of the genotypes I sent

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Structure Analysis

Hello everyone, I will perform a STRUCTURE analysis for the SNP marker file of the genotypes I sent

Jul 3

İLBİLGE OĞUZ, Terry Casstevens2

Jun 17

Kind request of TasselTutorialData5 zip.

This works for me https://tassel.bitbucket.io/docs/TASSELTutorialData5.zip On Mon, Jun 17, 2024 at 1:

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Kind request of TasselTutorialData5 zip.

This works for me https://tassel.bitbucket.io/docs/TASSELTutorialData5.zip On Mon, Jun 17, 2024 at 1:

Jun 17

Jun 12

Unable to load vcf file can you please help me with it

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Unable to load vcf file can you please help me with it

Jun 12

Jun 2

missing homozygous minor allele

Hello, May I ask, when I did Data -> Numerical Genotype on my vcf file, I don't see any

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missing homozygous minor allele

Hello, May I ask, when I did Data -> Numerical Genotype on my vcf file, I don't see any

Jun 2

Fazal Manan, … Hugo Cuevas11

May 19

Issue with uploading the file

Okay, I will try this ! Thanks a lot for the help Get Outlook for iOS From: tas...@googlegroups.com

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Issue with uploading the file

Okay, I will try this ! Thanks a lot for the help Get Outlook for iOS From: tas...@googlegroups.com

May 19

Zoë, Terry Casstevens5

May 17

BuilderFromPLINK error

If you want to send me your files privately, I can try it On Fri, May 17, 2024 at 10:57 PM Zoë <

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BuilderFromPLINK error

If you want to send me your files privately, I can try it On Fri, May 17, 2024 at 10:57 PM Zoë <

May 17

May 13

VCF file problem header - TASSEL 5

Hi, I have a .vcf file that I have generated using TASSEL and I am trying to run further analysis on

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VCF file problem header - TASSEL 5

Hi, I have a .vcf file that I have generated using TASSEL and I am trying to run further analysis on

May 13

Virginia Baraja, Terry Casstevens2

Apr 26

Heterozygous proportion estimated

Does this web page answer your question? https://bitbucket.org/tasseladmin/tassel-5-source/wiki/

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Heterozygous proportion estimated

Does this web page answer your question? https://bitbucket.org/tasseladmin/tassel-5-source/wiki/

Apr 26

Apr 26

rTassel in command line-PCA and accociation analysis

Hello, I am tryyin to use rTassel for Association analysis. I got the following error. Any solution

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rTassel in command line-PCA and accociation analysis

Hello, I am tryyin to use rTassel for Association analysis. I got the following error. Any solution

Apr 26

Apr 15

Problem Converting Hapmap to VCF

Hi All, I don't get any error for converting Hapmap to VCF in the Tassel. Also, when I open the

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Problem Converting Hapmap to VCF

Hi All, I don't get any error for converting Hapmap to VCF in the Tassel. Also, when I open the

Apr 15

Eduardo Beche, Brandon Monier2

Apr 11

rTASSEL ABH and numeric format

Hi Eduardo, Yes - when you import your genotype data, you can use R's base as.matrix() function

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rTASSEL ABH and numeric format

Hi Eduardo, Yes - when you import your genotype data, you can use R's base as.matrix() function

Apr 11

RN Sarma, … Agriculture Biotechnology Sadettin Soner ÇELİK6

Apr 9

Error in trait fille

Dear friend, İn columb o of excel there are two numbers. Please delete this columb. On Tue, Apr 9,

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Error in trait fille

Dear friend, İn columb o of excel there are two numbers. Please delete this columb. On Tue, Apr 9,

Apr 9

Mar 31

Intersect join related issues

Hi, I have been trying to Intersect join my genotype and phenotype files but fail. I am herewith

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Intersect join related issues

Hi, I have been trying to Intersect join my genotype and phenotype files but fail. I am herewith

Mar 31

Susheel Kumar Raina

Mar 31

Issues related to join intersection regd.

Hi, When I try to join intersect my genotype and phenotype files, no results are generated. The

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Issues related to join intersection regd.

Hi, When I try to join intersect my genotype and phenotype files, no results are generated. The

Mar 31

Vijay Rajamanickam

Mar 30

Association mapping /GWAS using SSR markers

Dear Folks, I would like to know the possibility of doing GWAS with SSR markers in TASSEL. regards,

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Association mapping /GWAS using SSR markers

Dear Folks, I would like to know the possibility of doing GWAS with SSR markers in TASSEL. regards,

Mar 30

Mao, Lynn Carol Johnson2

Mar 25

Any suggestions on the mem set up

Memory issues will depend on what memory is available on your system. In terms of TASSEL and GBSvs,

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Any suggestions on the mem set up

Memory issues will depend on what memory is available on your system. In terms of TASSEL and GBSvs,

Mar 25

Susheel Kumar Raina, Hugo Cuevas3

Mar 23

Unable to load phenotype data file

Dear Sir, Thank you so much for the guidance. I am humbled by your immediate response. I went through

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Unable to load phenotype data file

Dear Sir, Thank you so much for the guidance. I am humbled by your immediate response. I went through

Mar 23

Ryan Disney, Terry Casstevens3

Mar 15

Error Processing VCF block: Mismatch of alleles.

Thanks! That seems to have been at least part of the problem. I changed my script to modify the ALT

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Error Processing VCF block: Mismatch of alleles.

Thanks! That seems to have been at least part of the problem. I changed my script to modify the ALT

Mar 15

Daniel Tabas, … Terry Casstevens4

Mar 14

Problem with indels

Please follow these instructions to get more information. https://bitbucket.org/tasseladmin/tassel-5-

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Problem with indels

Please follow these instructions to get more information. https://bitbucket.org/tasseladmin/tassel-5-

Mar 14

venkat rami reddy

Mar 13

Different results if the dataset is used in intersect vs union join function

Hi all, I am using an association panel in 147 bread wheat lines to conduct GWAS. I attempted both

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Different results if the dataset is used in intersect vs union join function

Hi all, I am using an association panel in 147 bread wheat lines to conduct GWAS. I attempted both

Mar 13

Celia VI, … gsi...@ucdavis.edu12

Mar 11

GBSSeqToTagDBPlugin:processData problem in the key file

Hi Alden, It was the issue with the fastq file name having "text" vs "txt". Good

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GBSSeqToTagDBPlugin:processData problem in the key file

Hi Alden, It was the issue with the fastq file name having "text" vs "txt". Good

Mar 11

Zachary Winn, Lynn Carol Johnson6

Mar 11

Maj/Min vs Ref/Alt - Can I make sure my VCF comes out of production with Ref/Alt instead of Maj/Min coded?

Zachary – thank you for sharing this! From: tas...@googlegroups.com <tas...@googlegroups.com>

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Maj/Min vs Ref/Alt - Can I make sure my VCF comes out of production with Ref/Alt instead of Maj/Min coded?

Zachary – thank you for sharing this! From: tas...@googlegroups.com <tas...@googlegroups.com>

Mar 11

Владимир Александров, Terry Casstevens2

Mar 10

Problem with Intersect Joint function.

Please follow these instructions to get more information. https://bitbucket.org/tasseladmin/tassel-5-

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Problem with Intersect Joint function.

Please follow these instructions to get more information. https://bitbucket.org/tasseladmin/tassel-5-

Mar 10

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