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The following settings are available for all library types.
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Reference Genome
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The reference genome selected in the Planned Run.
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Library Type
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The default value is the library type selected in the Planned Run, and it can be changed only if the plugin is run manually. If you change the library type, a different report is generated.
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Targeted Regions
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The targeted regions are selected in the Planned Run, and can be changed only after the run is complete if the plugin is run manually. Target regions can be overwritten by the specific barcode targets.
Select the targeted regions file from the list. For whole genome and Ion Total RNA-Seq sequencing runs, you typically select None.
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Barcode-specific Targets
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This option is available only when the coverageAnalysis plugin is run manually.
Select the checkbox to assign specific target region files to individual barcodes.
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Select a specific barcode.
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Select the specific Target Regions file to associate with the selected barcode.
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Click Add.
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Repeat steps 1 through 3 to associate additional barcodes with specific Target Region files.
Alternatively, you can copy and paste the barcode/target file pairs manually.
Barcodes without a Target Region specified above assume the default target specified by the Target Regions option.
For targeted applications, any barcode targets specifically set to None, or defaulting to Target Regions set to None, are omitted from subsequent analysis.
When the Barcode-specific Targets option is deselected, all barcodes use the targets specified by the Target Regions, even if barcode-specific targets are listed.
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The following are advanced options.
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Minimum Aligned Length
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Specify the minimum aligned length that is required to ensure that the read is included in an analysis.
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Minimum Mapping Quality
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Specify a minimum value that reads must exceed to be included in the analysis.
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Tier 1 Coverage Depth
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Specify the first-tier coverage depth at which percentage of target coverage is reported. This value must be at least 2, because the coverage depth output is always specified at 1x read depth. The default value of 20 means that the percentage of targets, total base targets, and/or individual target bases with at least 20 reads is reported.
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Tier 2 Coverage Depth
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Specify the second-tier coverage depth at which percentage of target coverage is reported. This value must be greater than the value used for the first-tier coverage. The default value of 100 means that the percentage of targets, total target bases, and/or individual target bases with at least 100 reads is reported.
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Tier 3 Coverage Depth
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Specify the third-tier coverage depth at which percentage of target coverage is reported. This value must be greater that the value used for the second-tier coverage. The default value of 500 means that the percentage of targets, total target bases, and/or individual target bases with at least 500 reads is reported.
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The following settings are available only with specific library types.
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Uniquely Mapped Reads
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Select this option to analyze only reads that are mapped to a unique location in the reference. Reads that are non-uniquely mapped can have equally well-aligned reads that are mapped to multiple locations, and are typically mapped randomly to one.
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Sample Tracking
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The Ion AmpliSeq™ Sample ID Panel is a companion panel of 9 primer pairs that can be added to any Ion AmpliSeq™ human gDNA panel during target amplification to generate a unique identification tag for research samples. Select this checkbox if you added the Ion AmpliSeq™ Sample ID Panel to your library.
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Target Padding
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Enter a number to pad the target by the number of bases entered. If you do not enter a number, the default of 0 is used.
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Non-duplicate Reads
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Select the checkbox to avoid duplicates. The analysis must have included alignments with Mark Duplicates enabled.
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