To edit the STR Filter tab configuration
1. On the Viewer Options menu for the STR Analysis viewer, click Filter Settings.
The Filter Settings dialog box opens. The STR Stutter tab is the open tab.
2. Open the STR Filter tab.
3. Right-click anywhere in the tab pane and on the context menu that opens, click Open Table Config.
The context menu closes. The Table Configuration dialog box opens on top of the STR Filter tab. The dialog box displays all the fields that can be displayed on the tab in a default order. By default, all available fields are selected for display on the tab. The table below details all the fields (filter settings) that are available on the tab.
Filter Setting | Description |
|---|---|
Marker | The default is All, which means that all the STR filter settings are applied to all the markers for a project sample. |
Allele | The default is All, which means that all the STR filter settings are applied to all alleles for a project sample. |
Sequence AT Count | The number of reads that are required to pass the analytical threshold (AT). |
Sequence IT Count | The number of reads that are required to pass the Interpretive Threshold (IT), which results in the sequence being flagged as a possible allele. |
Sequence Allele AT Percent | The percent of total reads for an allele that are required to pass the AT, calculated as Sequence AT Count/Allele Count. |
Sequence Allele IT Percent | The percent of total reads for an allele that are required to pass the IT, calculated as Sequence IT Count/Allele Count. |
Sequence Marker AT Percent | The percent of total reads for a marker that are required to pass the AT, calculated as Sequence AT Count/Marker Count. |
Sequence Marker IT Percent | The percent of total reads for a marker that are required to pass the IT, calculated as Sequence IT Count/Marker Count. |
Maximum Sequence AT Balance | The balance is set to the greatest value out of the following calculations: • SequenceForward%/MarkerFoward% • MarkerForward%/SequenceForward% • SequenceReverse%/MarkerReverse% • MarkerReverse%/SequenceReverse% Note: Any balance value that is greater than the balance value that is set here is automatically filtered out, which means that the sequence is not called as an allele. To disable filtering, set the value here to inf. |
Maximum Sequence IT Balance | The balance is set to the greatest value out of the following calculations: • SequenceForward%/MarkerFoward% • MarkerForward%/SequenceForward% • SequenceReverse%/MarkerReverse% • MarkerReverse%/SequenceReverse% Note: Any balance value that is greater than the balance value that is set here and that is less than the Maximum Sequence AT Balance is automatically flagged as a possible allele. To disable flagging, set the value here to inf. |
4. Do any of the following:
• To show a field on the tab, select the check box in the Visible column.
• To hide a field from the tab display, clear the check box in the Visible column.
• To rearrange the order in which the fields are displayed in the results table, drag a field and drop it into its new location in the Unique Name (Fields) list.
As you edit the STR Filter tab configuration, the display is dynamically updated.
 | At any time that you are editing the STR Filter tab configuration, you can click File > Reset Columns to return the columns to their default order and/or visibility. |
5. After you are satisfied with the edited tab configuration, do one of the following:
• To immediately apply the changes to the STR Filter tab and return to the tab, close the Table Configuration dialog box.
• To save the configuration changes so that you can use them for other GeneMarkerHTS projects, on the Table Configuration dialog box, do the following:
a. Click File > Save Config As.
The Save Config dialog box opens.
b. Enter a name for the configuration file.
c. Optionally, select a different location in which to save the file. (By default, the location is set to the project folder.)
d. Click Save.
The Save Config dialog box closes and the Table Configuration dialog box remains open.
e. Close the Table Configuration dialog box.
The configuration changes are applied immediately to the STR Filter tab.