MARKERS»IMPORT

Description

• For a given population, observed allele size ranges can often be smaller than those defined in the marker sets Barley and Wheat. Users can import their own customised allele size range information to reflect this, allowing more efficient "binning" of markers.
• Use the MARKERS»IMPORT option to import files with marker allele size ranges into marker sets owned by the user.
• To edit allele size ranges for individual marker entries, or to delete individual markers from a marker set you have previously created, please refer to the EDIT and DELETE options in MARKERS»SEARCH.
• To import files with information for other fields in the MARKERS Table, please use the MARKER DB IMPORT option, available to group administrators (go to ADMIN»MY GROUPS to find out who to contact if you are not a group adminsitrator yourself).

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How to use this option

1. Create a tab-delimited text input file (see below) with allele size information for your marker set.
2. In MARKERS»IMPORT, use the BROWSE function to locate the input file created in step 1.
3. Either choose an existing marker set from the drop-down menu or create a new marker set by clicking on the [ADD MARKER SET] button. This will open an "Add Marker Set" interface where you can enter the name of the new marker set, select to which user group the new marker set is going to be assigned, and select whether viewing access to the marker set should be "private", "group-wide" or "public". After clicking the "Save" button, the new marker set is saved and you return to the "Import Marker" interface.
4. Click on IMPORT to upload the marker data.

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The MARKERS»IMPORT input file

• Creating an input file with the Automated Designer for Marker Screening:
  1. The Automated Designer for Marker Screening macro automatically creates a BINNER file. (See the GMT tutorial for full details on using the different available Automated Designer for Marker Screening macros.)
  2. Save the BINNER file (from the "polymorphism summary" worksheet) and use it directly as input file for MARKERS»IMPORT.
• Creating an input file without the Automated Designer for Marker Screening:
  1. Use a spreadsheet program to generate a table as shown below with the markers and their allele size ranges:
     • The allele size range for each marker is defined by the minimum and maximum allele size in base-pairs.
     • Each marker can have up to four allele size ranges. Use separate allele size ranges to describe markers amplifying multiple loci and / or to indicate "noise" regions, where non-specific PCR fragments are found that might interfere with scoring if another marker was allowed to co-occupy the region.
     • The table must not contain a header row.
     • It has been found useful to subtract 2 bp from the minimum allele size and add 2 bp to the maximum allele size when describing the size range for each marker. This adjustment to the allele size range for each marker ensures that GeneMapper is able to automatically call a microsatellite allele when stutter bands are present.
  2. Save the marker allele size data table as a tab-delimited text file (.txt) using the FILE»SAVE AS»SAVE AS TYPE»TEXT (TAB DELIMITED) (*.TXT) option of the spreadsheet program.

Example of a MARKERS»IMPORT Input File.
The first column contains the markers' names, followed by the sizes (in base pairs) of the minimal and maximal alleles defining up to four allele size ranges. Please note that the table must not have a header row.

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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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