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