Torrent Browser Analysis Report Guide

Introduction

A Torrent Browser run report contains statistics and quality metrics for your run. From a run report you can do the following:

Review pre-alignment metrics such as bead loading, Ion Sphere Particle (ISP) density, total number of reads, filtering numbers, and mean read length
Review alignment metrics such as total aligned bases, average coverage, and mean raw accuracy
Download the result set
Manually run a plugin on the run results
Review the planned run settings
Review the test fragments used with this run and test fragment quality metrics
Review analysis information and Torrent Suite Software versions
Review the analysis log
Generate a zip file for technical support

A run report is divided into the following main areas (see the example run report below):

Report header Buttons to download the run report or summary in PDF format, to review the planned run settings for the run, to reanalyze the run, and to upload the run's output files to Ion Reporter Software; a menu to change to a different result set for the same sample; and a navigation bar to jump to the Output Files or Plugin Summary sections.
Barcode Summary For barcoded runs, a barcode summary table appears above the Plugin Summary area.
Unaligned Metrics taken before alignment, including bead loading, ISP density and other metrics, read and filtering metrics, and read length
Aligned Metrics on the aligned reads
Plugin Previews Summary output of completed plugins (only if supported by the plugins that executed on this analysis)
Output Files Download buttons for reads both before alignment and after alignment (full-chip Ion Proton analyses only offer the download of aligned reads)
Plugin Summary Links to plugin reports and a button to select another plugin to run on this analysis
Test Fragments Displays information about the performance of each test fragment included in the experiment
Analysis Details Displays a set of information about the sequencing run environment (run date, sample name, chip type, instrument name, barcode set, etc.)
Support Displays a link to the report log and a link to generate information for technical support
Software Version Displays the version of Torrent Suite Software and its modules

The left side of a r un report header contains the following navigation links:

Run Summary Jumps to the Run Summary area
Output Files Jumps to the Output Files area
Plugin Summary Jumps to the Plugin Summary area (which also has the Test Fragment, Analysis Details, Customer Support, and Software Version buttons)

The right side of run report header contains buttons for the following:

Upload to IR Copies the run report's output files to Ion Reporter Software (see One-Click Transfer to Ion Reporter Software )
Report Actions
- Review Plan Opens a summary page of the planned run information for this run
- Edit Run Plan Opens an Edit Run page
- Copy Plan Opens the run plan wizard with a copy of the run plan information for this run
- Select plugins to run Opens the Select a plugin window
- Reanalyze Starts a reanalysis of the run (you have the opportunity to changes settings first)
- Data Management Opens the Data Management app, which you use to delete, archive, export, or mark as do-not-delete the files for this run report
Reports Opens the run report of a different result set for the same sample

- Summary PDF D ownloads the run report summary in PDF format
- Plugins PDF Downloads a summary of the plugin results in PDF format
- Classic Report Opens the run report in Torrent Suite Software 2.x format

Drop-down options shown below:

From a project listing page, you can compare report metrics for multiple runs side-by-side. See Compare Multiple Run Reports .

The Torrent Browser cannot display run reports from 2.x versions of the Torrent Suite Software in the current run report format.

To work with results generated with a 2.x version of Torrent Suite Software, you have these options:

Re-analyze the run to generate a new report Opens the Data > Completed Runs & Reports > Reanalyze page. Typically you click Start Analysis button to re-analyze with the same settings. The Advanced page is also available to change the analysis settings. After you re-analyze the run, you then have all 3.x features available in the new run report.
View the pre-3.0 report Open the run report in the old pre-3.0 style. Many new features are not available in the old style run report.
View this report log Open the text log for this run.

Contents