GMT Tutorial Exercise 10

Identify conflicting allele values in GEMDB

The "conflict finder" option allows searching for replicates that have been given inconsistent allele scores. Before comparing allele values, GMT automatically corrects them for dye drift and presence / absence of MRT tags.

1. Search for a dataset to be analysed. Demo file "GEMDB_import_example.txt" contains replicate allele values for the parental lines in a second run, called "2005-12-05_Plate1". Here, we will identify if any of the replicate allele scores differ from those in the first run ("2005-11-28_Plate1").
   1. Select GEMDB and then SEARCH.
   2. Select Tag: All
   3. Select Group: All
   4. Select Project: "your name_demo" created in Exercise 4, and where demo genotype data was imported in Exercise 5. Please ensure both exercises have been completed beforehand.)
   5. Select Run: All (to include both runs from this project)
   6. Leave all the "following" settings (Other, Marker, Allele, "¦) at their defaults or blank.
   7. Click Search.
2. View Results for this search.
3. Tag all results for this search.
4. Enter a new tag Name for this set of samples. Ensure the tag is a GEMDB TAG. Click Save.
5. Select GEMDB from the GMT menu, then select the CONFLICT submenu option.
6. From the GemDB Tag drop-down box, select the tag you have created in steps 3. and 4.
7. Select HELP to access the GMT online manual for details on the CONFLICT»FINDER display options, if desired. In this tutorial, use the default settings.
8. Click Analyse.
9. Depending on the size of the dataset, the conflict finder step can take some time. Results can be accessed at a later time through a link under "System Messages" on the ADMIN»DASHBOARD.
10. Review the conflict finder output; try moving the mouse cursor over allele values to see details on a data point in a "hover box" (see the screenshot below).
11. Try clicking on an allele score "“ note how this opens the GEMDB»BROWSE interface, filtered for the selected data point.
12. Try downloading the results "“ note the two different tables in the output file. One table has allele scores, one has datapoint details for each allele score, identical to the "hover box" entries.

• Tip: You can search for conflicting values across different groups, projects, etc. To do this, identify the different datasets to be compared in separate GEMDB searches and tag results for the different searches with the same GEMDB tag (ie don't enter a new tag name when tagging the second, third, etc. data set, but keep choosing the tag created for the first dataset in subsequent tagging rounds).
  
• Note that replicates are recognised based on Sample Name and Marker Name. If you wish to compare data sets, you have to ensure that identical naming conventions have been followed throughout.

The CONFLICT»FINDER results for the tutorial file. Detailed information on a data point is displayed in a "hover box" (in yellow) that appears when moving the cursor over the table entry.