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Torrent Browser User Interface Guide

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User Interface Guide TOC

Reanalyze a run

To begin a sequencing run, see Templates , Planned Runs , and Plan by Sample Set .

When you reanalyze, any setting changes you make affect only the current run (when you click the Start Analysis button). If you instead click Edit , your changes are saved for each subsequent reanalysis. See also Edit run metadata .

Start your reanalysis

You select the Reanalyze option either from the Completed Runs And Reports table or from a run report:

  • In the run report of a completed run, click the Report Actions > Reanalyze in the report header:







  • In the Data > Completed Runs & Results tab table view, click the Reanalyze option in the gear menu on the right of the run entry:



Follow these steps to reanalyze your run:

  1. Use one of the Reanalyze options.



  2. Enter the Report Name for the new run (required).



  3. To rerun the analysis with the same settings , fill in the report name and click Start Analysis .

    To rerun the analysis with changed settings, click the tabs on the left panel to display the analysis options and make your changes.

  4. Click Start Analysis to start the run, which checks the analysis status before displaying the run confirmation message:





  5. View run progress by clicking Report or by selecting the run name in the Monitor tab.



  6. Click Log to view run progress details in text form. Click your browser refresh button to update the log.

Settings tabs

When you reanalyze a run, you have to option to change the run's settings. Settings are organized by tab in the left panel:

The settings for your original run are displayed when you open these tabs.

The Reanalyze Run tab

In the Reanalyze tab, you enter a name for the new run report and the reanalysis starting point:

Setting Description
Report Name The name of the new run report (the result of the reanalysis).
Start reanalysis from

The Analysis Pipeline proceeds through three stages: Signal Processing, Base Calling, and Alignment. Normally report generation proceeds through all three steps, but if you have already generated a report, it is possible to reanalyze the experiment and skip the earlier stages of the pipeline.

For example, you may wish to change the genome that is used for Alignment. After changing the genome for the experiment on the Runs page using the Edit field, you need to reanalyze data to produce a new report using the new genome. But since there is no need to repeat the time consuming Signal Processing and Basecalling steps, you can use the output from an existing report as a starting point for Alignment, and the report will be completed much more quickly.

You can restart the analysis from these points:

  • Signal Processing (Default) Does not use the Use data from previous report field. Reprocesses from the DAT files. You can optionally use both the Analysis args and Basecaller args fields.
  • Base Calling Uses the Use data from previous report field and optionally the Basecaller args field. Reprocesses from the .wells file. Does not use the Analysis args field .
Use data from previous report This option applies only when starting reanalysis from Base Calling. In this case, the results from a previous report are used as input for reanalysis.

Analysis Parameters

Click Custom to view the Analysis Parameters page:

Setting Description

Beadfind args

Beadfind module command line arguments. Should not be modified unless instructed by Ion Torrent Technical Support.

Analysis args

Analysis command line arguments. Should not be modified unless instructed by Ion Torrent Technical Support.

Pre Basecaller args for calibration

BaseCaller command line arguments. See Basecaller arguments for information on --barcode-mode , --barcode-cutoff , and --barcode-filter . Other Basecaller arguments should not be modified unless instructed by Ion Torrent Technical Support.

This field is used only if the Enable Recalibration checkbox is enabled.

Recalibration Args

Recalibration command line arguments.

The Recalibration --skipDroop setting must match the BaseCaller --skipDroop setting. By default the BaseCaller and Recalibration consider both carry forward (cf) and incomplete extension (ie), but not droop (dr).

Basecaller args BaseCaller command line arguments. See Basecaller arguments for information on --barcode-mode , --barcode-cutoff , and --barcode-filter . Other Basecaller arguments should not be modified unless instructed by Ion Torrent Technical Support.
Alignment Args

Arguments for the TMAP aligner.

(Replaces the TMAP Args field that appears in previous releases.)

See TMAP Modules for information about TMAP parameters.

BaseCaller arguments

This section describes select arguments used with the BaseCaller module.

Argument Type Description
--barcode-cutoff

1.0

(Float)

Maximum distance allowed in barcode matches.A threshold that sets the stringency for barcode matches. Lower values require more exact matches when assigning reads to barcodes. Higher values allow less exact matches.

Reads that have a distance greater than this value are counted as barcode no-matches.

--barcode-filter

0.01

(Float)

Barcode frequency threshold to be reported in the UI.

Set to 0.0 to turn this filter off. The setting 0.0 causes all barcodes in the barcode set to be reported in the UI (including barcodes with no or very few reads).

--barcode-mode

2

(Integer)

Allowed values: 1, 2

  • 1 : A barcode is scored by comparing each read sequence to each barcode sequence in a flow space alignment. Errors in each flow are summed over the length of the barcode flows. Then any barcode with a number of errors equal to or less than the --barcode-cutoff value can be considered, and the barcode with the fewest errors with respect to the input sequence is the matching barcode. (The default in 4.0, known as hard decision classification.)

  • 2 : Barcode classification is based on signal information,specifically on the squared distance between the measured signal and the predicted barcode signal. (The default since 4.2, known as soft decision classification.)

Note : --barcode-mode 0 is no longer supported.

--barcode-filter-minreads

20

(INT)

Threshold for the minimum number of reads in a barcode group, for that group to be reported in the UI.

.

See BaseCaller Parameters for information about other, less-frequently-used parameters.

The Analysis Options tab

An example Analysis Options page is shown here:

The Analysis Options tab contains these settings:

Setting Description

Library Key

Sequence used to identify library reads. Example: "TCAG".

TF key Sequence used to identify test fragment reads. Example: "ATCG".

TF config

Name of an external file that specifies Test Fragment information. If a file is not specified, the default Test Fragment file is used.
3' Adapter The name and sequence of the 3' adapter.
Mark as Duplicate Reads Filter out PCR duplicates. Useful when reanalyzing combined BAM files. Do not use with Ion AmpliSeq data. See About the Mark as Duplicate Reads .
Base Calibration Mode Three options are available: Default Calibration, No Calibration and Enable Calibration Standard. See topic 'About the Base Calibration mode options' here: Wizard Kits Chevron .
Enable Realignment

Realignment is an optional analysis step that is executed right after TMAP. This step adjusts the alignment, primarily in the CIGAR string.

About the Mark as Duplicates Reads option

For some applications, duplicate reads coming from PCR cause problems in downstream analysis. The presence of duplicate reads may create the appearance of multiple independent reads supporting a particular interpretation, when some of the reads are in fact duplicates of each other with no additional evidence for the interpretation.

Torrent Suite Software uses an Ion-optimized approach that considers the read start and end positions by using both the 5' alignment start site and the flow in which the 3' adapter is detected. Duplicate reads are flagged in the BAM in a dedicated field. Use of the Torrent Suite Software method is recommended over other approaches which consider only the 5' alignment start site.

Marking duplicate reads is not appropriate for Ion AmpliSeq data, because many independent reads are expected to share the same 5' alignment position and 3' adapter flow as each other. Marking duplicates on an Ion AmpliSeq run risks inappropriately flagging many reads that are in fact independent of one another.

The Reference & Barcoding tab

The Reference & Barcoding tab contains these settings:

Setting Description
Default Alignment Reference The genomic reference to align to. Use this menu to change the reference used for alignment in the new analysis.
Default Target Regions BED File Targeted regions of interest file. Analysis is restricted only to regions listed in this file.
Default Hotspot Regions BED File Hotspots file. The variant caller includes each hotspot position in its output VCF file. Variant caller filter scores are provided for each hotspot position that does not have a variant called.
Barcode Set The DNA barcode set.
Icon

The BED file menus display only the BED files that are associated with the Alignment Reference. Choose your reference first.

See TMAP Modules for information about TMAP parameters.