GEMDB»IMPORT

Description

• Use the GEMDB»IMPORT option to upload molecular marker data for your research projects into GEMDB (currently restricted to SSR data in GeneMapper^® output format).
• If "?" (question marks) are used to identify null alleles in GeneMapper^®, 'GENica Marker Tools' can be used to convert these into "0" during the GEMDB»IMPORT.
• If "?" (question marks) are instead used to overwrite questionable allele calls in GeneMapper^®, 'GENica Marker Tools' can be instructed to remove these allele calls from the dataset.
• Users of the Multiplex Ready Technology (MRT) can indicate the presence of an MRT tag. 'GENica Marker Tools' can correct allele sizes to allow ready comparison with allele sizes obtained by conventional PCR, e.g. as reported in the literature.
• Data is rearranged to skip "empty" allele entries.
• During import, markers that do not already exist in marker sets Barley or Wheat in the MARKERS Table are recorded in a user-specified gemdb-type marker set. (Please also refer to the section on MARKER SETS.)
• Once imported, use GEMDB»SEARCH or GEMDB»BROWSE to search and, if required, edit the stored data.

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How to use this option

1. Identify a project in which the data is to be stored from the "Project/Group" pull-down menu. The menu displays the names of projects a user has access to, followed by the projects' user group names in brackets. Click on the [ADD PROJECT] link to create a (new) project. (Please also refer to the section on GEMDB»BROWSE.)
2. Use the "MRT Marker Set for missing markers" pull-down menu to specify a gemdb-type marker set where markers that do not already exist in marker sets Barley or Wheat in the MARKERS Table can be recorded. If you do not have access to a gemdb-type marker set, click on the [ADD MARKER SET] link to open the "Add Marker Set" interface where the marker set name and user group can be specified. gemdb-type marker sets can only be created with private access. (Please also refer to the section on MARKER SETS.)
3. Click on BROWSE to locate the input file to be uploaded.
4. Select the genotyping platform from the "Platform used" pull-down menu.
5. Select from the special import options:

   Convert all '?' alleles to 0 (null)?

   GeneMapper does not provide an explicit option for labelling a "null" allele. 'GENica Marker Tools' allows to overcome this restriction: If "null" alleles exist in the data set, these can be marked with "?" (question marks) in GeneMapper. By selecting the YES radio button in reply to this question, all '?' are converted to null alleles. By selecting the NO radio button, question marks in any of the "Allele" columns are interpreted as indicating missing data, even where the corresponding size, hight, etc., fields contain entries. Find out more...

   Multiplex Ready Technology?

   Identify whether data was generated using "Multiplex Ready Technology" or by "conventional PCR" by selecting the corresponding radio buttons. Find out more...

6. Enter a Run Name and a Panel Name if these fields are not provided in the GEMDB»IMPORT input file, e.g. when using the GeneMapper^® "Microsatellite Default" table settings. Please note that if the input file does contain entries in these fields, entering text through the GEMDB»IMPORT interface does not overwrite the entries in the input file.
7. Click on IMPORT to begin uploading the file. This may take some time, depending on the size of the input file.
8. An import report appears, giving details on the run that has been created.
   Click on the [DELETE UPLOAD] link if the wrong file has been imported.
   Click on the [DOWNLOAD IMPORT LOG] link if you wish to save an import log for future reference.
9. After reviewing the import report, click on the FINISHED button to complete the GEMDB»IMPORT. This will bring up the GEMDB»BROWSE interface, please refer to the GEMDB»BROWSE manual section for details.

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The GEMDB»IMPORT input file

• Currently, GEMDB is restricted to SSR data generated with GeneMapper^®. Please refer to Applied Biosystem's "Microsatellite Analysis - Getting Started Guide" or to "A Beginners Guide to Fragment Analysis Using GeneMapper^®" (prepared by Kylie Munyard and Marie Scobie at the Centre for High-throughput Agricultural Genetic Analysis, Murdoch University) for information on using GeneMapper^®.
• For every sample, up to 10 allele scores can be recorded. Please click here for a file with available GeneMapper column headings that can be used to characterise genotyping data in GEMDB.
• Please note that information in the following fields has to be provided as a minimum:
  • Sample File
  • Sample Name
  • Marker
  • Dye
  • Allele
  • Run Name^*
  • Panel^*

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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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