MARKERS»SETS

Description

• Select MARKERS»SETS from the 'GENica Marker Tools' menu to view and create marker sets.
• To view the markers in a marker set, select its name from the "Marker Set" drop-down menu that is available as one of the MARKERS»SEARCH Options.

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Information in the MARKER SETS table

• This screenshot shows the informaton on the MARKERS»SETS interface, details below.

Marker Set

This column lists the marker sets that you have access rights to.

Access

• public: Every 'GENica Marker Tools' user can view public marker sets.
• group: Every member of the user group this marker set belongs to can view its content.
• private: A private marker set can only be viewed and changed by the user who created it.

Set Type

• mrtmarker: This is the marker set type of the Wheat and Barley marker sets. Marker sets of this type have to be imported though the ADMIN»MARKER DB IMPORT function, available to group administrators. This function allows providing information for all the fields available for Multiplex-Ready^TM markers, see also information on the MARKERS database.
  Because mrtmarker marker sets contain information on allele size ranges, this set type can be used for binning MRT markers by allele size informtion and is therefore called binnable (see also section on BINNER»MRT TAGS).
  To create an mrtmarker type marker set, please read the section on ADMIN»MARKER DB IMPORT and contact your group administrator for help.
• binner: This is the set type for marker sets that have been created and uploaded for MRT binning purposes only, see the sections on BINNER»MRT TAGS and MARKERS»IMPORT for details on how this is done. binner marker sets contain allele size ranges for the markers and are therefore binnable. They do not contain extra information on primer sequences, marker quality, etc. found in the mrtmarker marker sets.
• gemdb: Marker sets of this set type have to be created before a user can import any genotyping data into GEMDB; the GEMDB»IMPORT interface has an [ADD MARKER SET] option to do this (see also the section on GEMDB»IMPORT). This type of marker sets exists solely to allow the import of genotype data for markers whose names do not exist in marker sets Barley or Wheat. A gemdb marker set does not contain any information on allele size ranges. This type of marker set is therefore non-binnable.
• DArT: This set type was created to import information on DArT^® markers with the ADMIN»DART MARKER DB IMPORT option. Only group administrators of user group "Triticarte" can use this import option.

Complete DArT® marker information for wheat and barley markers has not yet been released from Triticarte. Once this information becomes more readily available, we will attempt to display this data in DArT marker set Triticarte DArT Markers.

• snpmarker: Single Nucleotide Polymorphism (SNP) marker information can be imported into marker sets of this type with the ADMIN»SNP MARKER DB IMPORT option (available to group administrators). SNPBINNER uses marker information for snpmarker marker sets to group SNPs that can be analysed together in FlexMAP microsphere-based OLA ("oligonucleotide ligation assay") or ASPE ("allele-specific primer extension") assays on the Luminex. See the manual page on BINNER»SNP UPLOAD for details.

User Group

Name of the user group a marker set belongs to. Users belonging to different user groups can select to which of their user groups a marker set should belong.

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Browse the MARKERS»SETS table

• Use the [first], [prev], [next] and [last] buttons to move between pages of information (if applicable).
• Change the table order by clicking on the header of a column you wish to sort by.
• To change the number of lines displayed per page, edit your preferences (please refer to the section on OPTIONS).

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The EDIT and DELETE options

• Edit and delete options exist for marker sets created by the user. Group administrators have edit and delete rights to marker sets that were created any user in the group(s) they administer.
• Select [EDIT] next to a marker set to open an "Edit Marker Set" interface where the marker set's access setting can be changed.
• Select [DELETE] next to a marker set that you wish to delete. A "Delete Marker Set" interface appears, prompting the user to confirm or cancel this action.

IMPORTANT: By deleting a marker set, all the associated information in the MARKERS Table will also be deleted. Note that if a marker set contains markers for which genotype data exists in GEMDB, DARTS or SNPDB, it cannot be deleted.

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The ADD option

• To create a new binner-type marker set, select the [ADD] button at the lower right-hand side. This opens an "Add Marker Set" interface where the user group, name and access settings for a new marker set can be entered.
• To create a new marker set of another type, please refer to this overview on where to find relevant information:

mrtmarker-type

Create this type of marker set with the ADMIN»MARKER DB IMPORT option.

snpmarker-type

Create this type of marker set with the ADMIN»SNP MARKER DB IMPORT option.

gemdb-type

Create this type of marker set with the GEMDB»IMPORT option.

DArT-type

This type of marker set can only be created by GMT systems administrators.

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How to enter marker data into a marker set

• The MARKERS»SETS interface allows viewing and managing marker sets. To actually create and edit the marker data belonging to a marker set, the following options exist, depending on the marker set's "type":

Entering marker information into GEMDB type marker sets

• Select the gemdb marker set when importing genotype data into GEMDB (see also the section on GEMDB»IMPORT). The name of any marker in the genotyping dataset that doesn't already exist in either the Barley or the Wheat marker set is automatically added into the selected gemdb type marker set. No information on allele size ranges for these markers will be recorded.
• Marker information in a gemdb marker set can also be edited and deleted one at a time through the MARKERS»SEARCH interface (see section on the MARKERS»SEARCH EDIT and DELETE options).

Entering marker information into BINNER type marker sets

• To upload a text file with marker names and the related allele size ranges, refer to the section on the MARKERS»IMPORT function.
• Use the MARKERS»SEARCH interface to edit and delete entries one at a time (see sections on the MARKERS»SEARCH EDIT and DELETE options).

Entering marker information into MRTMARKER type marker sets

• Group administrators can upload a text file with information on marker names, primer sequences, allele size ranges, marker quality, etc., through the ADMIN»MARKER DB IMPORT function. Please contact your group administrator for help. To find out who is/are the group administrator(s) for your group(s), select ADMIN»MY GROUPS»[ADMINISTRATORS] from the 'GENica Marker Tools' menu.

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Entering marker information into SNPMARKER type marker sets

• Group administrators can upload a text file with information on marker names, primer sequences, FlexMAP tag numbers, etc., through the ADMIN»SNP MARKER DB IMPORT function. Please contact your group administrator for help. To find out who is/are the group administrator(s) for your group(s), select ADMIN»MY GROUPS»[ADMINISTRATORS] from the 'GENica Marker Tools' menu.

Entering marker information into DArT type marker sets

• Group administrators of user group "Triticarte" can upload a text file with information on marker names, chromosome location, etc., through the ADMIN»DART MARKER DB IMPORT function. Please contact group administrators from this group for help. To find out who is/are the group administrator(s) for user group "Triticarte", select ADMIN»MY GROUPS and click on [ADMINISTRATORS] next to "Triticarte".

Links to other user manual pages

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