GMT Tutorial Exercise 23 - Workflow 2 - Step 9

Using the macro - the PANEL File worksheet

The screenshot below shows the PANEL File worksheet that is opened when clicking on the Generate PANEL File button of the PCR Master Mixes worksheet.
This file will be required when analysing electrotraces in GeneMapper, see also further details below.
After ensuring this file has been saved, click on the Next Page button of the macro to move on to the next step of this workflow.

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 kit name with the experiment name, e.g. Tutorial_Example_Kit1 as shown above.
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, e.g. Tle_Kit1 as shown above.
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 wheat marker ta0217 amplifies two loci with expected PCR fragment size ranges of 254-269 and 294-364 bp. This SSR can be described within a panel file with the marker names:

 ta0217a	yellow	254	269	-	2	0	none
 ta0217b	yellow	294	364	-	2	0	none