BINNER»SNP TAGS

Description

• SNPBINNER groups a list of SNPs^* into "bins" that can be analysed together on the Luminex platform in FlexMAP microsphere-based oligonucleotide ligation assays (OLA) or allele-specific primer extension (ASPE). To do this, SNPBINNER applies the following four rules.
  • Binning Rule 1: Each FlexMAP "tag" can only occur once in a multiplexed assay
  • Binning Rule 2: Only one SNP on a given contig can be analysed in a multiplexed assay
  • Binning Rule 3: SNPs whose probes are known to form dimers are not multiplexed
  • Binning Rule 4: SNPs known to be amenable to probe / contig mispriming are not multiplexed
• Click on a binning rule for more details.

• BINNER»SNP TAGS allows to use markers that were "tagged" in MARKERS»SEARCH or in SNPDB»SEARCH as input.
• Use BINNER»SNP UPLOAD to use lists of markers saved as *.txt files as SNPBINNER input.

^*Single Nucleotide Polymorphism (SNP), definition:
A genetic marker resulting from variation in sequence at a particular position within a DNA sequence. SNPs can result from a base transition (A for G, T for C), transversion (G or A for T or C) or single-base deletion. Such variation is extensive throughout all genomes. (Pronounced "snip".)

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How to use this option

1. "TAG" the markers to be binned in MARKERS»SEARCH (find out how) or in SNPDB»SEARCH (find out how).
   • There is no limit to the number of markers you can tag and submit for binning.
   • In SNPDB»SEARCH, be sure to select a "SNPDB tag", not a "Sample tag" (what's this?).
   • You can view and delete markers that have been tagged in TAGS»MARKERS or in TAGS»SNPDB.
2. Go to BINNER»SNP TAGS and locate the tag created in step 1 from the "SNP Tags" drop-down box.
3. From the "SNP Set" drop-down box, select the marker set with the SNP marker information you want to use to bin the markers.
   • The marker set SNP Markers contains the default SNP marker information for all SNP markers implemented at the University of Adelaide.
   • Customised marker sets can equally be used; please refer to the section on ADMIN»SNP MARKER DB IMPORT for explanations on how a binnable SNP marker set can be created and imported.
4. If bins of a specific bin size are desired, enter a number in the Bin size text box.
   SNPBINNER will attempt to create bins of that size, while ensuring that the binning restrictions are applied. Currently, the biggest possible bin size is "12".
5. Start the binning process by clicking on the UPLOAD button.
6. Download the SNPBINNER result with the [Download results file] button.
   Alternatively, the table can be selected and copied straight from the webpage; in Excel, use the "Paste Special..." option and paste as "text".

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The SNPBINNER output

• The SNPBINNER result is displayed as a table with the bin number in the first column, followed by entries for the following fields (headers as used in the ADMIN»SNP MARKER DB IMPORT file, please refer to the linked manual page for details):
  • LabID
  • ASPEname
  • Contig
  • SNPname
  • SNP1allele
  • SNP2allele
  • SNP1LUA
  • SNP2LUA
• All the SNP markers with the same number in the first column can be analysed together on the Luminex platform in FlexMAP microsphere-based oligonucleotide ligation assays (OLA) or allele-specific primer extension (ASPE).
• SNPBINNER input parameters are displayed above the results table.
• Markers for which GENica Marker Tools could not identify binning information are listed as "Rejects". These can be unrecognised markers or markers for which entries in fields contig, SNP1LUA or SNP2LUA are missing, please also refer to these details on SNPBINNER function).
  Note:
  If all the markers in your list have been rejected, please verify that the correct marker set has been selected and that the correct marker names have been used in the SNPBINNER import file.
• An example of the SNPBINNER results table is shown below:

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Links to other user manual pages

I'd rather try the tutorial...

• Get started with the GMT Tutorial
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