BINNER»SNP UPLOAD

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.

• To bin markers whose names are saved in a *.txt list file, select BINNER»SNP UPLOAD from the 'GENica Marker Tools' main menu.
• If you wish to bin markers that you have "tagged" in MARKERS»SEARCH or SNPDB»SEARCH, please use the BINNER»SNP TAGS option.

^*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".)

Back to contents

How to use this option

1. Create an input file for the SNP markers to be binned and save it on your computer.
2. Navigate to the BINNER»SNP UPLOAD interface. Click on BROWSE and locate the input file created in step 1.
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".

Back to contents

The SNPBINNER input file

• Identify the markers you would like to bin, e.g. by searching the MARKERS Table for SNP markers (see section on MARKERS»SEARCH).
• Create a *.txt file with a list of the SNP markers you would like to bin, e.g. by selecting the "File"»"Save As"»"Save as Type"»"Text Document (*.txt)" option in Microsoft Excel, Microsoft Word or Windows Notepad.
• Use the entries under heading SNP Name (SNP View) or under Published Name (General View) (e.g. ABC14307_137[C/T]bot, ABC01648_385[C/T]bot, ...) to refer to each SNP marker.
• There is no limit to the number of markers that can be binned at a time.
• Ensure that the list has no header row.
• You can download BINNER_SNP_UPLOAD_input_file_example.txt from FILES»LIST ('GENica Marker Tools' login required) for a trial run of SNPBINNER.
• An example of a SNPBINNER input file is shown below:

ABC15164_387[T/G]top
ABC15164_273[G/T]bot
ABC18274_173[T/C]top
ABC18274_106[G/T]bot
ABC52326_276[G/A]bot
ABC52326_454[G/A]bot
Bmy1_R115C_115[G/A]bot
Bmy1_E165D_165[C/G]bot
Bmy1_A223V_223[T/C]top

Back to contents

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).
• The name of the input file and other 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:

Back to contents

Links to other user manual pages

I'd rather try the tutorial...

• Get started with the GMT Tutorial
  Log in to 'GENica Marker Tools'