ADMIN»DART MARKER DB IMPORT
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
through MARKERS»SEARCH.
Jbrueggemann 14:03, 22 November 2007 (WST)
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Description
- DArT® (Diversity Arrays Technology) markers were developed by the people at Diversity Arrays Technology P/L; DArT® genotyping services are offered to the wheat and barley community through their subsidiary, Triticarte P/L. Please refer to these companies' websites for information on the technology and on available services.
- This option allows providing data for every available DArT® field of the MARKERS Table, see the description of the input file below.
- This option is only available to group administrators of the "Triticarte" user group. Please contact Gregory Lott if you find DArT® marker information that needs to be corrected or updated.
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How to use this option
- Select ADMIN, then DART_MARKER_DB_IMPORT from the GMT menu.
- Select the "Triticarte DArT® Markers" marker set from the "DArT® Marker Set" drop-down box.
- Marker information that is imported with this option has to be added to a DArT®-type marker set. As DArT® markers are centrally curated by Triticarte, there is currently no generally available option for group admins and non-admin users to create personal marker sets with their own data.
- BROWSE for the input file with the marker data and hit IMPORT to begin uploading the data.
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The DArT® marker DB import file
- Below is an overview of the fields that can be used to import DArT® marker information into the MARKERS Table.
- You can download a tab-delimited text file with these column headers and one line of example data (DArT_MARKER_DB_IMPORT_FIELDS.txt) from FILES»LIST ('GENica Marker Tools' login required) to use as a template for preparing an imput file.
- Open this downloaded template file in a spreadsheet program and enter the required information for your markers, taking guidance from the example data in the template file and the field descriptions on this page. make sure to delete the line of example data before saving the file as a "tab-delimited" *.txt file.
| DArT® Marker DB Field:
| Data Type:
| Description:
| Example:
|
| Clone ID | Number | Clone ID as used by Triticarte | 12345
|
| Marker name | Text | Marker name as used by Triticarte. "w" and "b" signify wheat and barley, respectively, the next two letters are abbreviations for restriction enzymes used when generating the library a clone came from (e.g. P signifies PstI and t signifies TaqI), followed by a numeric marker number | wPt-4859
|
| Origin | Text | Lab or person who has created a marker | Triticarte
|
| Type | Text | Marker type | DArT
|
| GenBank accession | Text | GenBank accession as assigned by NCBI | BE438572
|
| Chromosome | Text | Name of the chromosome to which the marker has been mapped. Chromosome information is only available for those species for which some genetic maps have been constructed. For some markers that map to more than a single locus, there are multiple chromosome assignments | 7D
|
| cM | Number | Marker position in centiMorgan on the chromosome. These entries refer to locus positions on consensus maps created by Triticarte, if such maps are avaialable. | 145.9
|
| Putative Linkage | Text | Reported marker / trait associations | |
|
| Comments | Text | This field can be used for other generic comments on a marker. | |
|
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Links to other user manual pages
I'd rather try the tutorial...
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