ERCC Analysis plugin configuration

The configuration options for the ERCC Analysis plugin are described in the following table.

Setting	Description
Use only forward strand reads	Available when manually running the plugin.
Passing R-squared value	To optionally change the R-squared value to set a default value for the summary report screen, enter a value between 0 and 1 as your minimum acceptable R-squared value (a lower value is indicated by a red light in the summary report). The value you enter on the ERCC Plugin Configuration screen is used when the plugin is auto-run and when a user manually launches the plugin without entering a value. Users can override this value on a per-run basis when they manually launch the plugin.
Minimum transcript counts	The minimum number of reads that a given ERCC transcript must have to be included in the analysis.
ERCC pool used	Select the ERCC transcript pool used when preparing the library.
Barcodes of interest	Note: If you configure a Planned Run or Planned Run template to execute the ERCC_Analysis plugin, and your experiment uses the Ion Total RNA-Seq Kit v2, you must select a barcode option: Select IonXpressRNA if your experiment uses this kit. Select RNA_Barcode_None if your experiment does not use a barcode kit