Jasieniuk:Notebook/Apomixis in hybrid Rubus/2010/09/13

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GeneMapper allele calling

  • Stella -- Please confirm that seed plates A and B, as named in the plate files from August, correspond to plates 1 and 2 as listed in the "Seed Well Plate" Excel file.
  • In the "Seed Well Plate" file, all of the even-numbered H wells are listed as blank. However, in the results on GeneMapper, I am seeing alleles in these wells. Please clarify what is going on here.
  • Are the parent individuals on the older seed plates, or do I need to get the plates from the hybridization study out of the -80 freezer?

Results so far (missing one run due to syringe failure): Media: RUBapomixis100913_Genotypes_Table.xlsx

In this file, do-overs have been consolidated with the original runs. All of the seed samples from April-May are in this file because I haven't had the time yet to go through them and figure out which are the failed samples.

++ Stella ++

- 1: Seed well plate file also corresponds to those plates. A means plate 1, B means plate 2. Samples labeled "L" are the most recent leave samples, and if they are labeled "S" then those are the old seed runs, which are different from the current. In the current run, I did not do sample set name "BWP" because they were 80+% successful on the old seed run, and I still keep the old BWP dilution plate in the freezer.

- 2: In Genemapper, I admit I also saw allele in the H, and those are indeed blanks (probably spilled), and they are not parents.

- 3: The parent individuals are in the older leaf dilution plates, but not in the seed plates.

  • Before every run, I always make an INFO file in My Document/Stella in the sequencing computer. For example, if the name of plate is RUB100908, then the info file would be RUB100908_INFO. Those INFO file will show what is the real sample name for each sample.