The following settings are available for all library types.

Reference Genome

Reports reference genome specified in the planned run.

Library Type

Affects the type of report that is generated. Default value is the library type selected in planned run and can only be re-specified for manual run.

Targeted Regions

Affects type of report generated. Default region is the default target specified by the planned run and can only be re-specified for manual run. These target regions may be overwritten by the specific barcode targets.

Select the targeted regions file used during the run from the dropdown list. For Whole Genome and RNASeq application sequencing runs, you typically select None.

Barcode-specific Targets

Affects type of report generated for individual barcodes. Default targets are specified by the planned run and can only be re-specified for manual run. No reports are generated for individual barcodes that have target regions that are specified as None for targeted applications, as for example with the AmpliSeq DNA application.

Select the checkbox to assign specific target region files to individual barcodes.

1. Select a specific barcode from the barcode dropdown list.

2. Select the specific targeted regions file from the dropdown list to associate with the selected barcode.

3. Click Add.

4. Repeat steps 1–3 for each additional barcode you wish to assign a specific a target region file.

Minimum Aligned Length

Specify a minimum value that reads must exceed in order to be included in the analysis. Specify the minimum aligned length that is required to ensure that the read is included in an analysis.

Minimum Mapping Quality

Specify a minimum value that reads must exceed in order to be included in the analysis.

The following settings are available only with the library types indicated.

Sample Tracking

Only available with Ion AmpliSeq™ DNA, Ion AmpliSeq™ Exome, Ion AmpliSeq™ RNA, DNA and Fusions, and Tag Sequencing library types. Check this only if the Ion AmpliSeq™ library employed SampleID tracking amplicons.

Ion AmpliSeq™ Sample ID Panel (Cat. No. 4479790) is a companion panel of nine 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.

Target Padding

Only available with Generic Sequencing, TargetSeq and Whole Genome library types. Use to pad the target by the number of bases entered. If you do not enter a number, the default of 0 is used.

Use Only Uniquely Mapped Reads

Only available with Generic Sequencing, AmpliSeq™ DNA, AmpliSeq™ DNA and Fusions, AmpliSeq™ Exome, Tag Sequencing,TargetSeq and Whole Genome library types. For the plugin to examine unique starts only, select the checkbox.

Use Only Non-duplicate Reads

Only available with Generic Sequencing, TargetSeq and Whole Genome library types. Select the checkbox to avoid duplicates. The Torrent Suite™ Software analysis must have included alignments with Mark Duplicates enabled.