Edit the gene fusion analysis configuration file

For Oncomine™ fusion analysis workflows, a default analysis configuration file is provided. You can modify the file to set custom thresholds. For more information, see Analysis configuration file for gene fusion analysis.

  1. In the Workflows tab, click Overview.
  2. In the Workflows table, select the Oncomine™ fusion analysis workflow that contains the configuration file that you want to edit, then click  Actions > Copy and Edit for predefined analysis workflows, or  Actions Edit for custom workflows.
  3. Select a Research Application and Sample Group in the Edit workflow bar, then click Next.
  4. Click Parameters in the workflow bar, then select Fusions, then click the Advanced tab and scroll to the Analysis Configuration File section.
  5. Click Download to download the default analysis configuration file for the analysis workflow. The file name is appended with properties.txt.
  6. Save the file to a local directory, then open the file and make edits to any of the values for the following properties.

    • Minimum read count

    • Minimum normalized read count

    • Make calls

    • Minimum wild type ratio

    • Do not report

    • Maximum read count negative

    • Minimum molecular count (for use with AmpliSeq HD analyses)

    • Minimum Imbalance Score, for targets of type RNAExon Tile

    • Minimum Imbalance P value, for targets of type RNAExon Tile

    • Minimum average read count for Exon Tiling QC, for targets of type RNAExon Tile

    • Minimum wild type QC RNAExonVariants

    • Percent homology
    • Percent exact matches
    • Maximum weak amplicons
    • Minimum number of flanking amplicons for predicted RNATile breakpoint

    For more information, see Editable parameters in the analysis configuration file

  7. Save the file.
  8. In the Analysis Configuration File section of the Parameters workflow bar, click Upload.
  9. Browse to the updated file and select the file, then click Upload in the dialog.

The updated configuration file is added to top of the drop-down list in the Analysis Configuration File section of the analysis workflow parameters.

Related Topics
Parent topic: Analysis configuration file for gene fusion analysis