GMT Tutorial Exercise 23 - Workflow 2 - Step 7
Using the macro - the Marker Kit worksheet
- The screenshot below shows the Marker Kit 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) 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 four marker panels contains 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 a kit name for the GeneMapper panel file that this macro will generate
- Using kit names is 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.
(3) 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.
(4) 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
The Clear all information, except project details, sample names and GenMap file 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.
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