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The following settings can be configured when you run this plugin manually, or select it as part of a Planned Run or Planned Run template.
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Filter Barcodes
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Select this checkbox to remove whole barcodes from subsequent analyses if they have a relatively low number of reads, such as those that might 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.
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ERCC Tracking
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Select this checkbox if your
Ion AmpliSeq™ RNA targets (amplicons) were spiked with ERCC tracking targets. Typically, the Filter Barcodes option is not needed if your plan specifies which samples to associate with barcodes.
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The following settings can only be configured when you run this plugin manually.
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Reference Genome
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The short name of the reference genome (or DNA sequences) that the current run report was generated against. It will be used for coverage analysis. Typically this reference is an
Ion AmpliSeq™ Transcriptome reference.
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Library Type
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Select the library (enrichment type) what was sequenced. Currently only the
Ion AmpliSeq™ RNA lib type is available.
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Target Regions
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Select target regions to match your reference and enriched fragment library. Typically this will be an
Ion AmpliSeq™ Transcriptome target panel.
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