GMT Tutorial Exercise 23 - Workflow 2 - Step 6

Using the macro - the Project Details worksheet

• The screenshot below shows the Project Details worksheet of the "Automated Designer for Genetic Analysis, University of Adelaide Special Edition".
• Fill in the experimental details, following the instructions on this worksheet, see further explanations below.

(1) Enter a name for this project

• Entries in this field will be used by the Automated Designer when creating output files, helping to track different files used to set up and analyse a genetic analysis experiment.
• Because of their downstream use, entries in this field can only use a limited number of characters: Allowed characters: Regular letters (a-z); numbers (0-9); special characters: underscore (_) and dash (-).

Allowed, but undesirable character: full stop (.) (Use of full stops is undesirable, as they are usually interpreted as the separator preceding a file's extension. When presented with a file called e.g. "Sloop.Alexis.txt", the computer's operating system might have difficulty selecting the correct software application to open the file. Also, files with "double extensions" are usually considered high-risk by virus scanning software, making it potentially difficult to e-mail result files to collaborators.) Forbidden characters: All special characters, e.g. ü, é, æ, etc.; / \ & * # $ % , as well as spaces.

• A 3-letter "Project Abbreviation Code" is automatically created from the project name, by using the first, middle and last character of this entry. This "Project Abbreviation Code" is used as a pre-fix to create unique panel names that meet down-stream requirements imposed by GeneMapper 4.0.

(2) Enter the pedigree for the cross (if appropriate)

• Entries in this field are optional, this field is designed to store additional information on an experiment for future reference.

(3) Enter any comments required to historically document this experiment

• Entries in this field are optional, this field is designed to store additional information on an experiment for future reference.

(5) Paste in the box below the names of DNA samples to be used in this project in the order in which they occur in the 96- or 384-well extraction plates

1. Enter details on how DNA samples were stored after DNA extraction, by answering the three questions under instruction (5) (see below).
   This will update the plate and well references in the DNA sample box under heading Location on extraction plate, making it easier to copy / paste lists of DNA sample names from other electronic records.

   In what type of extraction plate are the DNA samples located?

   • Choose from "96-well" and "384-well", to reflect the way samples were stored after DNA extraction.

   In how many extraction plates are the DNA samples located?

   • As a maximum, up to 3840 DNA samples can be located on up to forty (40) 96-well plates, or on up to ten (10) 384-well plates.

   How are the DNA samples organised in the extraction plates?

   • Choose from "By Row" or "By Column", to reflect the order in which samples were stored after DNA extraction.




2. Copy / paste the names of DNA samples to be analysed in the genetic analysis in the column entitled DNA sample name.
   Double check that the DNA samples are properly aligned with entries under headings Extraction plate and Location on extraction plate, to ensure correct sample tracking.




3. In some instances, a user might want to pre-fix the DNA samples names with a consecutive number or similar, e.g. to control the order in which they appear when analysed in GeneMapper. If this is the case, enter a number or similar in the column entitled DNA sample number.
   • Note that entries in the DNA sample number column are optional.
   • Entries in the DNA sample number column will be prefixed to the entries under DNA sample name, with an underscore separator, e.g. "1001_Berkut".

The Next Page button

• After filling in the details above, click on this button to move on to the next step of using the Automated Designer macro.

The Reset Macro, Ready for a New Project button

• Click on this button to clear all information and start again. Occassionally, a macro can become corrupted and needs to be reset to work properly again. It's a good idea to re-save the reset macro with the Excel Save As... option before making a fresh start.