GENica MARKER TOOLS OPTIONS

The GMT OPTIONS interface is undergoing further changes. If you have any questions, contact Glott01

Description

• Use this mode of function to set display and export preferences.
• OPTIONS can be accessed directly on the 'GENica Marker Tools' main menu, or through the [SELECT COLUMNS] links displayed above the search results in GEMDB, DARTS and SNPDB, when the "Table View" has been selected.

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How to use this option

• Click on [EDIT] and choose from the available options (see below), then hit SAVE.

1. The "Pager Display Options"
2. The "Sample X Marker Page Display Options"
3. The "Search Display Options"
4. The "General Options"
5. The "Table Fields" Tabs

Pager Display Options

Lines Per Pager

• Specify how many lines are to be displayed per pager (min: 5 to max: 1000).
• Applies to all the pagers across 'GENica Marker Tools'.

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Sample X Marker Page Display Options

• The settings chosen in this section apply to the "SamplexMarker view" in GEMDB»SEARCH.




Alleles Per Marker

Available choices are 1 (e.g. for an all homozygous population) to 10.

Allele Values

• "Original": Allele values as imported into GEMDB.
• "Converted": Allele values corrected for dye drift (always) and for the length introduced by using multiplex-ready^TM markers (if applicable). To see an example of how allele values are converted in 'GENica Marker Tools', please click here.

MRT Marker Name

Tick this box if the column headers of the "SamplexMarker Table" are to display the multiplex-ready^TM marker codes (e.g. "hv0001"). This is available for markers htat are recognised as existing in marker sets Barley or Wheat during GEMDB import, based on a search of their names against the recorded MRT and published marker names in these marker sets.

MRT Published Name

Tick this box if the column headers of the "SamplexMarker Table" are to display the published marker names (e.g. "AB009307"). This is available for markers that are recognised as existing in marker sets Barley or Wheat during GEMDB import, based on a search of their names against the recorded MRT and published marker names in these marker sets.

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Search Display Options

• The settings chosen in this section apply to the "Table view" and the "Pager view" in GEMDB»SEARCH.




Alleles Per Marker

Available choices are 1 (e.g. for an all homozygous population) to 10.

Display Original Allele Values

Tick this box to display allele values as imported into GEMDB.

Display Converted Allele Values

Tick this box to display allele values corrected for dye drift (always) and for the length introduced by using multiplex-ready^TM markers (if applicable). To see an example of how allele values are converted in 'GENica Marker Tools', please click here.

MRT Marker Name

Tick this box if the GEMDB results are to be displayed with markers identified by their multiplex-ready^TM marker codes (e.g. "hv0001"). This is available for markers that are recognised as existing in marker sets Barley or Wheat during GEMDB import, based on a search of their names against the recorded MRT and published marker names in these marker sets.

MRT Published Name

Tick this box if the GEMDB results are to be displayed with markers identified by their pusblished marker names (e.g. "AB009307"). This is available for markers that are recognised as existing in marker sets Barley or Wheat during GEMDB import, based on a search of their names against the recorded MRT and published marker names in these marker sets.

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General Options

 Options to use alternative sample names in GEMDB are under development. To date, only the "Sample Name" option is available. 

Sample Name

Tick this box to display sample names as imported in the GEMDB»IMPORT input file.

Full Name

Tick this box to display alternative sample names, once this is available.

Export Format

• Choose from Tab-separated ".txt" and "comma-separated".
• Applies to all the exported files across 'GENica Marker Tools'.

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The Table Fields Tabs

• On the right-hand side of the OPTIONS interface, switch between different tabs, where the columns for the "Table Views" (or "Custom Views") in MARKERS»SEARCH, GEMDB»SEARCH, DARTS»SEARCH and SNPDB»SEARCH can be selected.




Marker Custom Fields

• The settings chosen on this tab apply to the "Custom View" of the MARKERS»SEARCH table. Whatever has been selected here will also be exported when downloading MARKERS data. (Click here for field descriptions.)




GemDB Table Fields

• On this tab, select the GEMDB database fields (columns) that you want displayed in the GEMDB»SEARCH "Table view". Whatever has been selected here will also be exported when downloading GEMDB data.




DArT Table Fields

• On this tab, select the DARTS database fields (columns) that you want to be displayed in the DARTS»SEARCH "Table View". The selected fields will also be exported when downloading DARTS data.




SNPDB Table Fields

• On this tab, select the SNPDB database fields (columns) that you want to be displayed in the SNPDB»SEARCH "Table View". The selected fields will be exported when downloading SNPDB data.

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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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