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.
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Save the file to a local directory, then
open the file and make edits to any of the values for the following
properties.
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Minimum read count
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Minimum normalized read count
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Make calls
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Minimum wild type ratio
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Do not report
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Maximum read count negative
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Minimum molecular count (for use with AmpliSeq HD analyses)
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Minimum Imbalance Score, for targets of type RNAExon Tile
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Minimum Imbalance P value, for targets of type RNAExon Tile
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Minimum average read count for Exon Tiling QC, for targets of type RNAExon Tile
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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
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- 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.
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