ampliSeqRNA plugin configuration

The configuration options for the ampliSeqRNA plugin are described in the following table. This plugin cannot be configured globally.

You can change the Reference Genome used in the plugin run, for example from hg19 to mm10, if you edit the run report, then reanalyze the raw reads. For details, see Edit a run report.

Alternatively, you can reanalyze the run. For details, see Reanalyze a run.

Setting	Description
The following settings can be configured when you select the ampliSeqRNA plugin as part of a Planned Run or Planned Run template.
Filter Barcodes	Select this checkbox to remove whole barcodes from subsequent analyses if they have a relatively low number of reads, such as those that can result from barcode contamination. A warning appears in the barcode summary report if any barcodes were discounted from the analysis. This setting is ignored for runs not employing barcodes. Typically, this option is not needed if your Planned Run specifies which samples to associate with specific barcodes.
ERCC Tracking	Select this checkbox if your Ion AmpliSeq™ RNA targets (amplicons) were spiked with ERCC tracking targets.

Setting

Description

The following settings can be configured when you select the ampliSeqRNA plugin as part of a Planned Run or Planned Run template.

Filter Barcodes

Select this checkbox to remove whole barcodes from subsequent analyses if they have a relatively low number of reads, such as those that can result from barcode contamination. A warning appears in the barcode summary report if any barcodes were discounted from the analysis. This setting is ignored for runs not employing barcodes.

Typically, this option is not needed if your Planned Run specifies which samples to associate with specific barcodes.

ERCC Tracking

Select this checkbox if your Ion AmpliSeq™ RNA targets (amplicons) were spiked with ERCC tracking targets.

Setting	Description
The following settings can be configured when you run the ampliSeqRNA plugin manually.
Library Type	ampliSeqRNA is selected automatically and is currently the only library type that the ampliSeqRNA plugin is designed to work with. If the Planned Run specified a different application, a message warns you that the plugin may not be appropriate for the run.
Targeted Regions	This is set by default to the target regions file used in the Planned Run. You can override the default setting that each barcode uses. This might be useful to specify a subset of genes of interest, or to correct the original Planned Run.
Filter Barcodes	Select this checkbox to remove whole barcodes from subsequent analyses. Typically, this option is not needed if your Planned Run specifies which samples to associate with specific barcodes.
ERCC Tracking	Select this checkbox if your Ion AmpliSeq™ RNA targets (amplicons) are spiked with ERCC tracking targets.

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ampliSeqRNA plugin configuration