TASSEL - Trait Analysis by Association, Evolution and Linkage

Contact owners and managers

1–30 of 2227

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.

0 selected

Virginia Baraja, Terry Casstevens2

Apr 26

Heterozygous proportion estimated

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

unread,

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

unread,

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

unread,

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

unread,

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,

unread,

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

unread,

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

unread,

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,

unread,

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,

unread,

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

unread,

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

unread,

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-

unread,

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

unread,

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

unread,

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>

unread,

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-

unread,

Problem with Intersect Joint function.

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

Mar 10

Jc Pineda, Peter Bradbury5

Mar 4

Association Analysis > Genomic Selection: Error 260 using Tassel Tutorial Data (Tassel 5.2.93, MacOS)

Accuracy_mdp_traits contains the results for each fold x iteration and can be exported and plotted

unread,

Association Analysis > Genomic Selection: Error 260 using Tassel Tutorial Data (Tassel 5.2.93, MacOS)

Accuracy_mdp_traits contains the results for each fold x iteration and can be exported and plotted

Mar 4

Eduardo Beche, Brandon Monier8

Mar 2

Error installing rTASSEL

It looks like you have a 64-bit version of R installed. I suggest reinstalling Java to ensure you

unread,

Error installing rTASSEL

It looks like you have a 64-bit version of R installed. I suggest reinstalling Java to ensure you

Mar 2

ban4...@gmail.com, … Agriculture Biotechnology Sadettin Soner ÇELİK3

Feb 20

converting hapmap with .csv format to .hmp.txt format

Hello Load in tassel 3. Then export as hapmap. On Mon, Feb 19, 2024, 16:56 ban4...@gmail.com <

unread,

converting hapmap with .csv format to .hmp.txt format

Hello Load in tassel 3. Then export as hapmap. On Mon, Feb 19, 2024, 16:56 ban4...@gmail.com <

Feb 20

yaman.jab, mvuyeni nyasulu3

Feb 16

Phenotyping file

Thank you very much Sent from my Samsung Galaxy smartphone. -------- Original message -------- From:

unread,

Phenotyping file

Thank you very much Sent from my Samsung Galaxy smartphone. -------- Original message -------- From:

Feb 16

yaman.jab, mvuyeni nyasulu5

Feb 16

Qualitative traits

I send you message on whatsapp Sent from my Samsung Galaxy smartphone. -------- Original message ----

unread,

Qualitative traits

I send you message on whatsapp Sent from my Samsung Galaxy smartphone. -------- Original message ----

Feb 16

Vijay Rajamanickam

Feb 10

Filtering in TASSEL- regarding

Dear Folks, Is it fine to set the following criteria (in the image) for filtering and quality control

unread,

Filtering in TASSEL- regarding

Dear Folks, Is it fine to set the following criteria (in the image) for filtering and quality control

Feb 10

Isabel Werle, … Peter Bradbury3

Feb 9

FSFHap to ABH format

No. There is not a tool in TASSEL to make that conversion. You will either need to do that yourself

unread,

FSFHap to ABH format

No. There is not a tool in TASSEL to make that conversion. You will either need to do that yourself

Feb 9

Vijay Rajamanickam, Terry Casstevens2

Feb 7

filtering genotype data

Maybe you want to set "Site Min Count" to the number of taxa? On Wed, Feb 7, 2024 at 2:50

unread,

filtering genotype data

Maybe you want to set "Site Min Count" to the number of taxa? On Wed, Feb 7, 2024 at 2:50

Feb 7

Hrithik Mangla L- A26

Feb 7

Error with the FSHAP imputation command

/home/gbsuser/GBS/tassel/tassel-5-standalone-new-hinpI/run_pipeline.pl -h CHR1.hmp.txt -

unread,

Error with the FSHAP imputation command

/home/gbsuser/GBS/tassel/tassel-5-standalone-new-hinpI/run_pipeline.pl -h CHR1.hmp.txt -

Feb 7

Feb 1

Adding row to ABH Genotype output file to dictate position of marker on chromosome

Hello! I am running R/QTL following the use of the Tassel ABH Genotype function to produce a .csv

unread,

Adding row to ABH Genotype output file to dictate position of marker on chromosome

Hello! I am running R/QTL following the use of the Tassel ABH Genotype function to produce a .csv

Feb 1

Feb 1

FSFHap without parents

Hi, I have an F2 population resulting from self-fertilization of a cross of homozygous parental line.

unread,

FSFHap without parents

Hi, I have an F2 population resulting from self-fertilization of a cross of homozygous parental line.

Feb 1

Isabel Werle, Peter Bradbury2

Feb 1

FSFHap Imputation - Pedigree file

The BC option is for backcross, so leave it un-checked. The parent contribution only applies to the

unread,

FSFHap Imputation - Pedigree file

The BC option is for backcross, so leave it un-checked. The parent contribution only applies to the

Feb 1

Rachel Tavares, Terry Casstevens4

Jan 29

All unknown N nucleotide values reported when loading VCF file

You need to remove the quotation marks from your file On Mon, Jan 29, 2024 at 4:04 PM Rachel Tavares

unread,

All unknown N nucleotide values reported when loading VCF file

You need to remove the quotation marks from your file On Mon, Jan 29, 2024 at 4:04 PM Rachel Tavares

Jan 29

Rachel Tavares, Terry Casstevens9

Jan 29

Load VCF file issue, ABH Genotype question

I found the problem using a text editor and was able to open the VCF after modifications. Thank you!

unread,

Load VCF file issue, ABH Genotype question

I found the problem using a text editor and was able to open the VCF after modifications. Thank you!

Jan 29

Search

Clear search

Close search

Google apps

Main menu