DARTS»IMPORT

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.
• Use the DARTS»IMPORT option to upload your DArT^®genotyping data into DARTS.
• Once imported, use DARTS»SEARCH or DARTS»BROWSE to search and, if required, edit the stored data.

Back to contents

How to use this option

1. Select DARTS, then select IMPORT, to reach the DARTS»IMPORT interface shown in the screenshot below.
2. Click on Browse and select the file to be imported. See details on the DArT^® input file below.
3. If desired, create a new project for the data to be imported with the [ADD PROJECT] link. Once a group, name and access settings for the new project have been entered, return to the DARTS»IMPORT screen by clicking the Save button.
4. Select the Project / Group under which to store the data to be imported.
5. Choose the Platform Used or leave as 'unknown'. If the import file has an entry in the platform field, this entry will be used instead of the platform entry on the DARTS»IMPORT screen.
6. Click Import.
7. Either wait for the import results, or retrieve them from the ADMIN»DASHBOARD "System Messages" box at a later time.
8. A table with details for the import appears.
9. Click Finished. The DARTS»BROWSE interface opens automatically, where imported data can be reviewed.

Back to contents

The DARTS»IMPORT interface.

The DARTS»IMPORT input file

• "Historically", DArT^® data has been reported in a number of different formats. To accommodate all of these, an "extended" format is used when importing DArT^® data into GENica Marker Tools. Please download the file "DARTS_IMPORT_FILE_TEMPLATE.txt" from the FILES»LIST interface (GMT password access required, please contact Gregory Lott for a user account) and use this as a template for your own data.
• Data has to be imported as a tab-del.txt file. In your spread sheet program (e.g. Excel), use the "Save as" option and then choose "Text file (tab-del.)" from the "Save as type:" drop-down box.
• Entries from different plates can be imported as separated txt files, or by copy pasting the data belonging to different plates next to each other, after ensuring that the markers are identical for the different plates. An example for how this can be done is given in the "DARTS_import_example.txt" file, available from the FILES»LIST interface (GMT password access required). Note the "Plate" field entries "pop x" and "pop y".
• The screenshot below shows an example for a correctly formatted DARTS import file, with required entries in blue, optional entries in green.
  • Required entries:

    Triticarte service

    Service number as assigned by Triticarte.

    Performed For

    Client / user name.

    Date

    Date entries should be made in the format "1-Apr-2007"

    Plate

    DNA is often submitted on more than one plate to Triticarte. In this field, a plate name needs to be supplied.

    marker name

    or "clone id" At least one of these has to be supplied, with "marker name" being the preferred one. Occasionally, however, data is reported for clones that have not been given a marker name yet. In that case, the "clone id" should be supplied.

    Sample names

  • Optional entries: (Although an entry may be optional, please do not delete the corresponding "header" from the import file.)

    Platform

    species

    barcode

    col

    If available, this field can be used to record the column where a DNA sample was stored on the microtitre plate analysed by Triticarte.

    row

    If available, this field can be used to record the row where a DNA sample was stored on the microtitre plate analysed by Triticarte.

    comment

    This field can be used to record information on a marker's performance in the given study. Entries in this field can be searched and displayed in DARTS»SEARCH. Use the "comments" field e.g. when a number of markers have been separated from others by an empty row and a comment in the original DArT^® report file (e.g. "second choice", "distorted segregation"). Then, this comment should be copied before each of the affected markers and the empty row should be removed before the data is imported into DARTS.

    p

    clonename

    genbank accession

    chromosome

    cM

    marker quality

    Note that in some older report files, this field was labelled "Q".

    call rate

    pic

    Allele scores

    Allowable allele scores are "1", "0" and "-" for missing data. Some older files use "X" to indicate missing data, if this is the case, the "x" will be automatically replaced with "-" during import into GMT.

DArT^® data in the import format recognised by GMT. "Blue" entries are required, "green" entries are optional.

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'