Automatic transfers of sequencing run data

Samples are typically transferred to Ion Reporter™ Software based on the settings that are selected in Torrent Suite™ Software. These settings, which are in the Ion Reporter step of the Planned Run in Torrent Suite™ Software, determine how the sample data file is transferred.

• If the Upload Only option is selected, the IonReporterUploader plugin automatically transfers the sample file, or files, for the completed sequencing run from the IonReporterUploader plugin to Ion Reporter™ Software without running data through an analysis workflow. A BAM file is transferred for all sequencing runs. If the variantCaller plugin was set up in the Planned Run, a VCF file is also generated, and transferred. After the transfer is complete, you must add the sample file or files to a sample definition in Ion Reporter™ Software and manually launch an analysis before you can review analysis results. For more information, see Sample definition and Manually launch an analysis.

• If instead, the Select an Ion Reporter™ Software workflow for your sample type option and an analysis workflow are selected in Torrent Suite™ Software, the transfer occurs based on which additional Ion Reporter Upload option is selected:

  • The Automatically upload to Ion Reporter after run completion option allows you to go directly to the analysis results in Ion Reporter™ Software. In this case, the sample data and analysis workflow settings are used to analyze the data.

  • The Review results after run completion, then upload to Ion Reporter option allows you to first review the sequencing run report in Torrent Suite™ Software, then manually upload the BAM file, the VCF file, or both files. With this option, you can evaluate the sequencing run before you transfer sample data and analyze the data in Ion Reporter™ Software. After you upload the BAM file, you must add one or more files to a sample definition in Ion Reporter™ Software, then launch an analysis to review analysis results. For more information, see Sample definition Launch an analysis.