GMT Tutorial Exercise 21 - Workflow 1 - Step 18
Using the macro - the Polymorphism Summary worksheet
- Follow the instructions on the Polymorphism Summary worksheet to complete the marker screening analysis.
- Click the Create BINNER and import files button and ensure that the BINNER and the GenMap file created from this worksheet are saved in the folder directory that was specifically created for the experiment.
(See examples for these output files below.)
- The files created with this worksheet are input for BINNER and for the Automated Designer for Genetic Analysis macro when setting up a genetic analysis, e.g. of a mapping population.
Using the marker screening results helps to...
- ...leave out non-informative markers when doing a genetic analysis experiment,
- ..."pack" markers more efficiently, hence reducing the number of capillaries needed to analyse samples,
- ...ignore non-informative "peaks" during GeneMapper scoring.
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Example BINNER output file
- The macro creates a file whose name is a combination of the entry on this worksheet (made following instruction 1 on the worksheet) and the extension _BINNER.txt. See an example BINNER file below.
- The first column contains the name of MRTTM markers that were analysed in the experiment.
- The following columns (up to 8) give the minimum and maximum allele sizes (in base pair) of up to four "allele size ranges".
- In the illustration below, e.g. "ta0217" (entry highlighted in green) has two allele size ranges, the first ranging from 256 bp to 267 bp, the second one ranging from 296 bp to 362 bp.
- The allele size ranges in this output file are as observed in the "marker screening" experiment. Unlike the "generic" information in the MRTTM marker database, they are specific for the DNA samples whose marker data was compared (see the "Primer Screening Analyser" worksheet).
- The 'custom' allele size ranges can be smaller than the 'generic' ones, making for more efficient "binning".
- Peaks can also be observed outside the generic allele size ranges, in this case, the adapted BINNER file ensures they will be included in GeneMapper "panel" files in subsequent genetic analyses.
- The BINNER output file can be used directly with the GENica Marker Tools BINNER application. Please refer to the instructions for the Automated Designer for Genetic Analysis macro.
ta0166 335 345
ta0217 256 267 296 362
ta0232 292 302
ta0352 339 355
ta0353 299 324
ta0471 255 348
ta0545 119 146 182 192
ta0647 215 225
ta0651 68 160
ta0656 196 264 466 485
ta0659 193 230
ta0669 114 176 298 359
ta0679 193 229
ta0682 171 181 291 302
ta0685 168 198 219 238
ta0688 127 148
ta0691 110 184
ta0701 313 361
ta0710 195 262
ta0823 123 172
ta0839 194 294
ta1044 127 148
ta1242 122 174
ta1614 164 309
ta1640 335 352
ta2267 256 266
Example GenMap output file
- The macro creates a file whose name is a combination of the entry on this worksheet (made following instruction 1 on the worksheet) and the extension _GenMap.txt. See an example GenMap file below.
- The first column contains the name of MRTTM markers that were analysed in the experiment.
- The following columns (up to 4) give the "polymorphism rating" for the "allele size ranges" (up to four) defined in the BINNER file
- In the illustration below, e.g. "ta0217"'s first allele size range is monomorphic, the second allele size range is polymorphic, both ratings have been automatically made.
- The polymorphism ratings in the GenMap output file are specific for the DNA samples whose marker data was compared (see the "Primer Screening Analyser" worksheet).
ta0166 p*
ta0217 m p
ta0232 p*
ta0352 p
ta0353 p
ta0471 p
ta0545 p m*
ta0647 p*
ta0651 p
ta0656 p p
ta0659 p
ta0669 p p
ta0679 p
ta0682 p* m
ta0685 p p
ta0688 p
ta0691 p
ta0701 p
ta0710 p
ta0823 p
ta0839 p
ta1044 p
ta1242 p
ta1614 p
ta1640 p
ta2267 p*
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