GEMDB»IMPORT options
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Import example for CONVERT ALL "?" TO "0" (NULL) ALLELE option
Description:
- GeneMapper does not provide an explicit option for labelling a "null" allele. 'GENica Marker Tools' allows overcoming this restriction: If "null" alleles exist in the data set, these can be marked with "?" (question marks) in GeneMapper. By selecting the YES radio button in reply to this question, all '?' are converted to null alleles.
- By selecting the NO radio button, question marks in any of the "Allele" columns are interpreted as indicating missing data, even where the corresponding size, height, etc., fields contain entries.
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Example: Input file with a question mark for "Allele 4":
| Sample File | Sample Name | Marker | Dye | Allele 1 | Size 1 | Allele 2 | Size 2 | Allele 3 | Size 3 | Allele 4 | Size 4 | Allele 5 | Size 5 | Allele 6 | Size 6 | Allele 7 | Size 7 | Allele 8 | Size 8 | Allele 9 | Size 9 | Allele 10 | Size 10 |
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| XYZ.fsa | XYZ | M1 | B | 100 | 100.3 | 120 | 119.7 | |
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| 127.3 | | | 155 | 154.5 | | | | | 170 | 170.3 | 200 | 200 |
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The input file after import with "CONVERT ALL ? TO 0 (NULL)?" set to "YES"
Note that "Allele 4" has been converted to a "null" allele (highlighted with a green arrow).
(Click on the image to see it enlarged.)
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The input file after import with "CONVERT ALL ? TO 0 (NULL)?" set to "NO"
Note that "Allele 4" has been left out (allele numbers are highlighted with a green frame).
(Click on the image to see it enlarged.)
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Import example for MULTIPLEX READY TECHNOLOGY option
Description:
- When using "Multiplex Ready Technology" (MRT) to PCR-amplify polymorphic genomic regions, the size of the resulting fragments is increased by an "MRT tag" that can vary between 30 bp and 38 bp, depending on the "multiplex-ready" marker used.
- By selecting the "YES" radio button for the "MULTIPLEX READY TECHNOLOGY?" option, 'GENica Marker Tools' is instructed to calculate "corrected allele" sizes, without the extra length introduced by the MRT tag. This allows comparisons between allele sizes obtained with "multiplex-ready" markers and by conventional PCR (e.g. as published in the literature).
- The allele size from the input file is recorded as "Allele", the re-calculated size is recorded under the column heading "Converted Allele". Which of these columns is searched can be specified in GEMDB»SEARCH; which one is displayed can be specified in 'GENica Marker Tools' OPTIONS.
- Regardless of whether MRT or conventional PCR was used, allele sizes are always corrected for "dye drift" effects, as illustrated in this example.
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Example: Input file with data for a multiplex-ready marker, labelled with different dyes (Green, Blue, Yellow, Red):
| Sample File | Sample Name | Marker | Dye | Allele 1 | Size 1
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| XYZ.fsa | XYZ | ta0003 | G | 100 | 100
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| XYZ.fsa | XYZ | ta0003 | B | 99 | 99
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| XYZ.fsa | XYZ | ta0003 | Y | 100 | 100
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| XYZ.fsa | XYZ | ta0003 | R | 102 | 102
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The input file after import with "MULTIPLEX READY TECHNOLOGY?" set to "NO (CONVENTIONAL PCR)"
Note the difference between the columns entitled "Allele" and "Converted Allele". In this example, the size differences in the input file are solely due to the use of different fluorescent dye labels, the so-called "dye drift":
Whereas the fluorescent dyes referred to as "Green" (VIC) and "Yellow" (NED) have no effect on allele size (in the example, both are n = 100), "Blue" (FAM) makes alleles appear 1 base "shorter" (n-1 = 99 in this example) and "Red" (PET) leads to allele scores increased by 2 (n+2 = 102 in this example).
'GENica Marker Tools' reverts these dye drift effects when calculating the "Converted Allele". This "dye drift" correction is done whether an MRT tag is present or not.
(Click on the image to see it enlarged.)
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The input file after import with "MULTIPLEX READY TECHNOLOGY?" set to "YES"
Note the difference between the columns entitled "Allele" and "Converted Allele". Allele sizes are corrected both for dye drift effects (see section above) and for the presence of an MRT tag.
For the multiplex-ready marker "ta0003", the MRT tag length is 38 bp, subtracting this from the allele size in the input file (100 bp without dye drift effects) results in a "Converted Allele" size of 62 bp.
(Click on the image to see it enlarged.)
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Links to other user manual pages
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