GMT Tutorial Exercise 23 - Workflow 1 - Step 6

Using the macro - the Data Entry worksheet

• The screenshot below shows the Data Entry worksheet of the "Automated Designer for Genetic Analysis", standard edition.
• Fill in the experimental details, following the instructions on this worksheet, see further explanations below.

(1) Paste in the box below four (4) marker panels, created by the BINNER software. Each marker panel can contain up to six (6) markers. To minimise wastage of PCR consumables, try to ensure that each of the marker panels contain a similar number of SSRs.

• Copy / paste the BINNER output generated in the BINNER step of this workflow, as shown in the screenshot example above.
• If the BINNER output has more than four panels, select four panels with similar numbers of SSRs, if possible. In the example below, the panels number 3-6, each containing 3 markers (panels and markers highlighted in green), would be a suitable selection:

1	ta0685	168	198	219	238	
1	ta1044	127	148	
1	ta2267	256	266	
1	ta0232	292	302	
1	ta0166	335	345	
2	ta0710	195	262	
2	ta1242	122	174	
2	ta0353	299	324	
2	ta0352	339	355	
3	ta0839	194	294	
3	ta0651	68	160	
3	ta0701	313	361	
4	ta0471	255	348	
4	ta0691	110	184	
4	ta0659	193	230	
5	ta0217	256	267	296	362	
5	ta0823	123	172	
5	ta0679	193	229	
6	ta1614	164	309	
6	ta0688	127	148	
6	ta1640	335	352	
7	ta0545	119	146	182	192	
7	ta0647	215	225	
8	ta0656	196	264	466	485	
8	ta0669	114	176	298	359	
9	ta0682	171	181	291	302	

(2) Enter the name of this experiment

• 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.

(3) Enter a kit name for the GeneMapper panel file that this macro will generate

• Using kit names is particularly useful to distinguish results when more than one "marker kit" (each consisting of up to 4 marker panels with up to 6 markers each) is to be analysed.
• It is not necessary to include an experiment reference with the kit name; the Automated Designer for Genetic Analysis will automatically prefix the experiment name to the entry in this field in order to create unique chemistry kit names as required by GeneMapper 4.0.

(4) Upload GenMAP file from 'Automated Designer for Marker Screening' (if applicable)

• If polymorphic markers have been selected in a marker pre-screening experiment, upload the GenMAP file generated by the Polymorphism Summary worksheet of the marker screening macro (either the "Automated Designer for Marker Screening" or the "Automated Designer for Whole Genome Scan").
• The name of the GenMAP file ends in *_GenMap.txt, and the file should have been saved in the directory that was created for the "marker screening" experiment.
• The information in the GenMAP file allows ignoring non-informative (monomorphic) allele size ranges when scoring markers in GeneMapper.

(5) Enter the PADDING (in base-pairs) used to construct the BINNER marker panels

• This refers to the Padding setting that was used in the BINNER step of this workflow.
• For pre-screened markers, the padding distance is normally set to "5 bp". If unsure, open the downloaded BINNER output file. The Padding setting that was used to generate the output is reported above the binning results.

The "Next Page" button

• Select this to move to the next worksheet in the macro.

The "Clear all information, except sample file data" button

• After the Automated Designer for Genetic Analysis has been used to design an experiment with a first "Kit" of up to four (4) marker panels, containing up to six (6) markers each, the macro can be used to set up an experiment with another "Kit" of markers.
• Click on this button to update only the marker information, but keep the DNA sample names and well positions that were already entered for the first kit.

The "Reset Macro" 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.