Reanalyze a run

You can reanalyze a run to correct a setup error such as a default reference alignment or an assigned barcode, or to optimize analysis parameters.

Torrent Suite™ Software provides two ways to change the options used to analyze sequencing data. If you want to change the options for the results of a sequencing run one time, you can change the options in the run report, then immediately reanalyze the data. If you want to change the run report for all future reanalyses of the data, you can edit the run report and save the updated report.

  1. In the Data tab, click Completed Runs & Reports.
  2. Search, filter, or sort the list to find your run report of interest. For more information, see Search for a run report.
  3. Do one of the following:

    • In Table View mode, in the row of the run of interest, click  (Actions) > Reanalyze.

    • Alternatively, switch to List View mode, find your run of interest, then click Reanalyze.

  4. In the menu on the left, click Reanalyze Run, enter a Report Name for the new run, then select from the available options.

    Option

    Description

    Thumbnail only

    Select to reanalyze only the thumbnail report. This option is available only for Ion Proton™ System, Ion S5™ System, and Ion GeneStudio™ S5 Systems data.

    Start reanalysis from

    • Select Signal Processing to reanalyze from DAT files.

      The analysis does not use the Use data from the previous result option, but reprocesses from the DAT files. You can also use Analysis and Base Calling options.

    • Select Base Calling (default) to reanalyze from 1.WELLS files.

      The analysis uses the Use data from the previous result or Base Calling options, but reprocesses from the 1.WELLS file. The analysis does not use the Analysis Parameters option.

    Use data from previous result

    Select the previous result if more than one result is available. This option applies only when starting reanalysis from the basecalling step.

    Analysis Parameters

    Use the default analysis parameters, or click Custom to select the analysis parameters.

    For more information, see Copy an analysis parameter set.

  5. (Optional) In the menu on the left, click Analysis Options, then set the options as needed.

    Option

    Description

    Library Key

    The sequence that is used to identify library reads.

    TF Key

    The sequence that is used to identify test fragment reads.

    3′ Adapter

    The sequence of the 3′ Adapter that is used.

    Mark as Duplicate Reads

    Select to have PCR duplicates flagged in the BAM file.

    Base Calibration Mode

    Base calibration mode allows for empirical alignments to influence flow signals to achieve better homopolymer calibration to improve overall accuracy.

    Enable Realignment

    Select to use an optional analysis step to adjust the alignment, primarily in the CIGAR string.

  6. (Optional) Set the reference and barcoding options.
    1. In the menu on the left, click Reference & Barcoding, then click Edit Run Plan.
    2. On the Edit Run Plan screen, set the default options as needed.
    3. Click Update Run to return to the reanalyze setup screen to select plugins to use in the analysis.
    4. If you do not need to return to the setup screen to change the plugins, click Update Run and Reanalyze.
  7. (Optional) In the menu on the left, click Plugins.
    1. Select the plugin to include in the reanalysis.
    2. (If needed) Click the Configure link next to the plugin, scroll down to configure the plugin, then click Save Plugin Settings.

      For more information, see Plugin configuration, or the configuration topic specific to the selected plugin.

    3. Repeat steps a and b to include additional plugins in the reanalysis.
  8. Click Start Analysis.
Related Topics
Parent topic: Review and manage run reports
Child Topics
Change the default alignment reference