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Sample names for the 2017 samples, which will be used for GBS and 16S/ITS, were provided in the Excel spreadsheet, by collaborators at the University of Tennessee. Populations were encoded with color! In March 2021, Alex Buerkle wrote a R script to read from the Excel sheet and encode population numbers in the sample ids.

  1. utenn_alfalfa_alfalfa_endophyte_2017.xlsx

  2. utenn_alfalfa_alfalfa_endophyte_2017.csv

  3. fix_alfalfa_xls.R

Shannon Harris Gregg Randolph : could you please run the fix_analysis_xls.R script yourself and examine the fixed.alfalfa object for possible errors in encoding the populations, which I had to do by hand? Please document any changes that need to be made and please let Alex Buerkle know.

Templates:

Template info from Erin Bentley as Google Sheet, or attached here on as a text file.

Plate Name

Samples

GBS Prep

Needed

GBS Prep

Completed

16S/ITS

Needed

16S/ITS

Completed

ALF_PLT1_2017_GBS

96

Y

Y

N

ALF_PLT2_2017_GBS

96

Y

Y

N

ALF_PLT3_2017_GBS

96

Y

Y

N

ALF_PLT4_2017_GBS

96

Y

Y

N

ALF_PLT5_2017_GBS

96

Y

Y

N

 

ALF_PLT6_2017_GBS

96

Y

Y

N

 

ALF_PLT7_2017_GBS

96

Y

Y

N

 

ALF_PLT8_2017_GBS

96

Y

Y

N

 

ALF_PLT9_2017_GBS

96

Y

Y

N

 

ALF_PLT10_2017_GBS

96

Y

Y

N

ALF_PLT11_2017_GBS

29

Y

Y

N

ALF_PLT1_2020_GBS

96

Y

Y

N

 

ALF_PLT2_2020_GBS

96

Y

Y

N

 

ALF_PLT3_2020_GBS

96

Y

Y

N

 

ALF_PLT4_2020_GBS

96

Y

Y

N

 

ALF_PLT5_2020_GBS

96

Y

Y

N

 

ALF_PLT6_2020_GBS

96

Y

Y

N

ALF_PLT1_2020_END

96

Y

Y

Y

 

ALF_PLT2_2020_END

96

Y

Y

Y

 

ALF_PLT3_2020_END

96

Y

Y

Y

 

ALF_PLT4_2020_END

96

Y

Y

Y

 

ALF_PLT5_2020_END

96

Y

Y

Y

 

ALF_PLT6_2020_END

96

Y

Y

Y

 

ALF_PLT7_2020_END

96

Y

Y

Y

 

ALF_PLT8_2020_END

96

Y

Y

Y

 

ALF_PLT1_2020_EPI

96

N

Y

ALF_PLT2_2020_EPI

96

N

Y

ALF_PLT3_2020_EPI

96

N

Y

ALF_PLT4_2020_EPI

96

N

Y

ALF_PLT5_2020_EPI

96

N

Y

ALF_PLT6_2020_EPI

96

N

Y

ALF_PLT7_2020_EPI

96

N

Y

ALF_PLT8_2020_EPI

96

N

Y

3101

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