Running and Verification

Procedure

1. Use PuTTY to log in to the server as the root user.
2. Go to the source package directory.

   cd /path/to/tassel/tassel-5-standalone

3. Calculate the kinship matrix.

   ./run_pipeline.pl -fork1 -h TASSELTutorialData/data/mdp_genotype.hmp.txt -ck -export kinship.txt

4. Calculate the LD analysis.

   ./run_pipeline.pl -fork1 -h TASSELTutorialData/data/mdp_genotype.hmp.txt -ld -ldd png -o chr_5000sites_ld.png
   ./run_pipeline.pl -fork1 -h TASSELTutorialData/data/mdp_genotype.hmp.txt -ld -export LD_5000sites

5. Extract chromosomes.
   • Extract each chromosome.

     ./run_pipeline.pl -fork1 -h TASSELTutorialData/data/mdp_genotype.hmp.txt -separate -export chromosome

   • Extract chromosomes 1 and 3.

     ./run_pipeline.pl -fork1 -h TASSELTutorialData/data/mdp_genotype.hmp.txt -separate 1,3 -export chromosome

6. Perform MLM analysis.

   ./run_pipeline.pl -fork1 -h TASSELTutorialData/data/mdp_genotype.hmp.txt -filterAlign -filterAlignMinFreq 0.05 -fork2 -r TASSELTutorialData/data/mdp_traits.txt -fork3 -q TASSELTutorialData/data/mdp_population_structure.txt -excludeLastTrait -fork4 -k TASSELTutorialData/data/mdp_kinship.txt -combine5 -input1 -input2 -input3 -intersect -combine6 -input5 -input4 -mlm -export lilibei -runfork1 -runfork2 -runfork3 -runfork4