GMT Tutorial Exercise 21 - Workflow 1 - Step 11

Using the macro - the PANEL File worksheet

This screenshot shows the Panel File worksheet of the "Automated Designer for Whole Genome Scan", see also further explanations below.
Click on Save PANEL file and "yes" at all following prompts to save the panel file. The macro will automatically save the panel file in the same directory where the macro is saved. The file name will be "_panelFILE.txt" appended to the experiment name (as entered on the Data Entry worksheet).
The panel file will be required to analyse electrotrace data in GeneMapper in a later step of this workflow.
If you wish to have a printed record, click on Print Preview.

If required, open the Automated Designer for Whole Genome Scan macro for your experiment and enable macro functions as described previously in this workflow.
Use the Save As... option and re-save the macro without changing its name or location. Click yes at the "file overwrite" warning. This step is required to ensure that macro-generated files are saved in the same directory as the macro.
Use the Next Sheet / Previous Sheet buttons on each worksheet to find the PANEL File worksheet shown above.

The analysis of samples by GeneMapper requires a number of tools, which are known as chemistry kits, panels, analysis methods, and sample and genotype tables. These tools must be related to the raw data generated by the ABI instrument before the samples can be analysed. Please refer to Applied Biosystems' GeneMapper^® documentation, e.g. their guide to microsatellite analysis.
A "panel" describes the markers that are contained within a capillary on an ABI instrument. It also contains information for the expected fragment sizes of each marker, and the dye detection channel in which each marker occurs. A typical panel file is shown below.

There are several important rules that the macro applies when writing panel files:

The name of the panel folder (the "chemistry kit") must be unique, i.e. it cannot have been previously used in GeneMapper. A good way to ensure this is to include the date or an experiment reference number in the panel folder name. The macro automatically prefixes each chemistry kit name with the experiment name.
The name of each marker panel has to be unique within GeneMapper, and each marker within a panel must be unique. Note that even if a panel name is saved in a part of the GeneMapper (version 4.0) database that is not actually visible to a user, the user cannot use that panel name. The macro automatically prefixes each panel name with a 3-letter code, derived from the experiment name.
Each marker can only have one expected fragment size range. Hence, PCR markers amplifying multiple loci must have a separate "marker" name defined for each locus. For example, the barley marker hv0034 amplifies two loci with expected PCR fragment size ranges of 254-257 and 322-324 bp. This SSR can be described within a panel file with the marker names:
- hv0034a blue 254 257 - 2 0 none
- hv0034b blue 322 324 - 2 0 none
Within a dye detection channel, marker fragment size ranges cannot overlap.