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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.

There will be additional samples beyond what is listed below (as of ). We expect on the order of 3647 samples for ITS and 16S preps and sequencing.

GBS only preps

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

16S/ITS preps

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