Torrent Browser User Interface Guide

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Torrent Suite Software space on Ion Community

User Interface Guide TOC

Plan Tab

The Plan tab gives you control over your sequencing experiments. You use a plan template, in the Plan > Template tab, to create a digital protocol with specifications for almost your entire experiment, from sample preparation through sequencing, data analysis, and data export to other systems for additional analysis. From the template, you create one or more planned runs, which execute directly on your Ion S5, Ion PGM , or Ion Proton sequencing instrument.

These steps describe how templates and planned runs fit into your Ion S5, Ion PGM, or Ion Proton sequencing workflow:

1. You decide on your sequencing application and sequencing product (such as an Ion AmpliSeq panel).
2. You select a pre-installed templatewith defaults for your application and sequencing product, or you create your own template from scratch. You customize your template.
3. You copy the template to a new planned run, adding the name of the tissue sample to be sequenced.
4. The Torrent Browser assigns your new planned a run code.
5. You enter the run code directly on the Ion sequencing instrument to initiate the sequencing.
6. The planned run automates the process from sequencing through data analysis and data handling.

In the Plan > Templates tab, you create and organize your templates, and also create planned runs. The Plan > Planned Runs tab lists existing planned runs. In this tab, you can review planned run settings and edit or delete planned runs.

The Plan tab in 4.4 offers a drop-down menu to speed you access to pages of interest.

Plan by sample set

You can also plan by sample set. In this case, you start on your sample set page, click the Plan Run gear menu option, and select your workflow template. Then the wizard reads the sample set and auto-populates the sample information (including barcodes, if any) in the wizard.

The plan-by-sample-set features is meant for the following scenarios:

• To set up a multi-sample analysis for Ion Reporter Software.
• To simplify the process of specifying large numbers of samples in the run plan wizard.

Plan-by-sample-set offers these benefits:

• It imports your sample attributes and sample relationships into the run plan.
• Data entry is easier in the sample set page than in the run pan wizard.

Plan Multiple

Use this feature to create multiple planned runs from your template. See Create Multiple Run Plans . ( Recommended for users who are familiar with templates and run plans.)

See also

See Templates , Planned Runs , Plan by Sample Set , Create Multiple Run Plans .

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