GMT Tutorial Exercise 23

The Automated Designers - How to use the genetic analysis macros

• The "genetic analysis" macros are used to analyse an unlimited number of DNA samples (e.g. representing a segregating population, or from a set of germplasm to be analysed for genetic diversity) with up to four marker panels, each composed of up to six MRT^TM markers.
• The Automated Designer for Genetic Analysis can be used on its own or after markers have been pre-screened.
  Please refer to instructions for the Automated Designer for Marker Screening or the Automated Designer for Whole Genome Scan for information on pre-screening markers.
• Two different "genetic screening" macros exist, a Standard version and a University of Adelaide version. The latter was customised to suit local user preferences. General users should choose the "Standard Edition". Step-by-step instructions for using either are found below. (Please contact Julia Brueggemann if you are interested in this version. It is not distributed through the GENica Marker Tools website. Jbrueggemann 07:45, 16 September 2009 (UTC))
• Click on a step for details. Move between the steps forming a workflow with the [previous step] and [next step] links in the top right-hand corner of each step-wise instruction.

Workflow 1: The Automated Designer for Genetic Analysis - Standard Edition

Select Markers and create BINNER panels

1. Choose MRT^TMmarkers for the genetic analysis.
2. Use BINNER to develop marker panels for the selected markers.

Design the experiment

3. Download the Automated Designer for Genetic Analysis macro from GMT.
4. Open the macro and enable the macro functions.
5. Check the macro's version number.
6. Using the macro - the Data Entry worksheet.
7. Using the macro - the PCR Master Mixes worksheet.
8. Using the macro - the PANEL File worksheet.
9. Using the macro - the DNA Samples worksheet.
10. Using the macro - the SAMPLE File.

Carry out marker assays

11. Prepare PCR products.
12. Separate PCR products on the ABI3730.

Score marker data

13. Import panel information into GeneMapper.
14. Import sample electrotraces into GeneMapper and determine peak sizes.
15. Score marker data in GeneMapper.
16. Export the GeneMapper marker data table.

Workflow 2: The Automated Designer for Genetic Analysis - University of Adelaide Special Edition

 Please contact Julia Brueggemann if you are interested in this version. 
 It is not distributed through the GENica Marker Tools website. 
 
 Jbrueggemann 07:49, 16 September 2009 (UTC)

Select Markers and create BINNER panels

1. Choose MRT^TMmarkers for the genetic analysis.
2. Use BINNER to develop marker panels for the selected markers.

Design the experiment

3. Download the Automated Designer for Genetic Analysis macro from GMT.
4. Open the macro and enable the macro functions.
5. Check the macro's version number.
6. Using the macro - the Project Details worksheet.
7. Using the macro - the Marker Kit worksheet.
8. Using the macro - the PCR Master Mixes worksheet.
9. Using the macro - the PANEL File worksheet.
10. Using the macro - the SAMPLE file worksheet.
11. Using the macro - the DNA Sample Sorter worksheet.
12. Review the Sample File.

Carry out marker assays

13. Prepare PCR products.
14. Separate PCR products on the ABI3730.

Score marker data

15. Import panel information into GeneMapper.
16. Import sample electrotraces into GeneMapper and determine peak sizes.
17. Score marker data in GeneMapper.
18. Export the GeneMapper marker data table.