I have run 479 polymorphic SSR makers on wheat genotypes. I dont know how to arrange marker data / phenotypic and K data in format of TASSEL 5. I want to do MLM and GLM analysis in TASSEL 5. kindly guide me for it.
Here are a few lines from each of the files (k-matrix, genotypes, phenotypes).
K-matrix should be a full matrix of relatedness, but also have the number of strains / individuals / accessions at the top.
Genotypes here are in HapMap format, but there are other formats. The first several columns (after the identifier) don't need to be filled in. TASSEL takes other formats as well (VCF, others) but this should help get you started.
Phenotypes are tab-delimited and can be continuous data, the example I pulled from is binary (0 or 1) but they can be decimals. You'll probably want to turn your phenotypes into a normal distribution, as this is often an expectation of MLM analyses (worth trying).
Feel free to reach out with questions.
Dear Sudhir
This link help you:
https://bitbucket.org/tasseladmin/tassel-5-source/wiki/UserManual/Load/Load
If you need further assistance you can contanct me.
Hi,
in the manual , you will find all examples of data..
https://bitbucket.org/tasseladmin/tassel-5-source/wiki/UserManualg
Good luck
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