Torrent Browser Analysis Report Guide

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Torrent Suite Software space on Ion Community

Analysis Report Guide TOC

The FileExporter Plugin

You use the FileExporter plugin to rename Torrent Suite Software results files and optionally to create FASTQ, SFF, or zipped versions of the results files.

This plugin replaces the FastqCreator and SFFCreator plugins.

Plugin output

The plugin output section shows the input options and provides links to the files that the plugin created or renamed:

The SELECTIONS area shows the file naming pattern used for this run. This example uses the naming pattern Run Name, Sample Name, and Report Date:

Run Name Auto_user_B22-884--26953

Sample Name E129294--L-

Report Date 2013-09-17

Plugin configuration

Configuration scope

You can configure the FileExporter plugin in two places. The configuration options are the same in both places. Only the scope of the configuration is different.

• In the manual launch page The configuration affects only that specific run.
• In the admin Plugins tab The configuration affects all automatic FileExporter runs by all users.

Manual launch

On a manual launch, the Select plugins to run button opens the plugin configuration page.

Admin Plugin tab

Configure FileExporter here to set up a file naming pattern and output file options to be used with all automatic FileExporter runs. This configuration affects FileExporter runs that are set up in the run plan and template wizard.

To access the admin plugin configuration area, click the Torrent Browser gear menu Plugins option:

Then click the Manage column gear menu for the specific plugin and select Configure :

Output file options

In the Output File Options section, you select the following options:

In this release, if launched with no file options selected, the plugin creates FASTQ and SFF files.

Plugin naming pattern (required)

This section describes how to set a file naming pattern in the FileExporter plugin. The naming pattern is used for the results BAM and BAI files, the SFF and FASTQ files, and the VCF results files (depending on the output file options selected).

You can use the following run metadata in your file naming patterns:

• Run Name
• Report Name
• Report Date
• Chip Type
• Sequencer Name
• Sample ID
• Barcode Name

You also can choose the delimiter used between metadata fields. Support delimiters are dot, dash, and underscore (a naming pattern uses only only one delimiter):

As you build your naming pattern, the Example name string section shows you the current pattern:

Follow these steps to create your file naming pattern in the Customize file names section. This example uses the following file naming pattern: Report Name.SampleID.Report Date.

1. Select the delimiter dot:
   
   
   
   
2. In the Field 1 menu, select the first part of the naming pattern. This example uses Report Name:
   
   
   
   
   
   Both Field 1 and the example name string show Report Name (TSP_ANALYSIS_NAME.bam is an internal name for Report Name):
   
   
   
   
   
   
3. Click the Add another field button. In the Field 2 menu, select Sample ID :
   
   
   
   
   
   Field 2 shows Sample ID and the example name string shows Report Name.SampleID (using internal names):
   
   
   
   
   
   
4. Click the Add another field button. In the Field 3 menu, select Report Date :
   
   
   
   
   
   Your file naming pattern is ready to use.
   
   
   
   

Note: The FileExporter plugin takes no action if you do not specify a file naming pattern.

Run the plugin automatically

You set up the plugin to run automatically when you configure your template or run plan. In the Plugin chevron of the template wizard, you select which plugins run automatically on planned runs created from that template. See the Templates page in the Torrent Browser User Interface Guide .

Important: Before you use the plugin in a planned run, configure the plugin in the admin Plugins page. A run template and planned run accept the plugin when it is not configured, but your plugin fails at run time.

Run the plugin manually

You can launch the plugin manually from a completed run report.

Follow these steps to run the plugin manually:

1. Open the run report and scroll down to the Plugin Summary button. Click Select plugins to run .
   
   
   
   
   
   
   
   
2. In the Select a plugin list, click FileExporter . Select your output file options and configure the file naming pattern.
   
   Note: In this release, you must configure a file naming pattern.
   
   
   
   
3. Click Submit .

Notes

• If you run the plugin multiple times on the same run report, the zip includes all output files from the previous FileExporter runs.
• VCF files are not included in the zipped file.
• In this release, if launched with no file options selected, the plugin creates FASTQ and SFF files if those files have not already been created.

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