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Torrent Suite Software space on Ion Community

User Interface Guide TOC

Create Samples and a Sample Set

The sample sets feature helps Ion Reporter Software users by automatically entering sample information into the run plan wizard.

This page explains how to create a sample set and how to add samples. You can add samples either through a CSV file that contains the sample information or manually in a popup form.

When you add samples manually in the popup, they are not saved until you explicitly save the sample set. This model is somewhat like a shopping cart: you can add, edit, change, and delete, and then save the sample set when you are finished.

Please read the Sample relationships and group number section before you add your samples.

A sample can be a member of more than one sample set.

Sample information

This table describes the fields in the Add Samples popup. The same fields are used in a CSV file that is imported to create samples.

Use the Add Sample popup

Follow these steps to add samples one-by-one in a Torrent Browser popup:

1. Go to the main Sample Sets page in the Plan > Samples tab. Click the Enter Samples Manually button.
   
   
   
   
2. In the Enter Samples page, c lick the Enter New Sample button. The Add Sample popup opens:
   
   
   
   
   
   
   
   
   
   See Sample information for a description of these fields and your entries.
   
   The Role and Relationship Group fields are described in the Sample relationships and group number section.
   
   Click Done to add the sample.
   
   
   
   
3. The Enter Samples page opens again, with your new sample listed:
   
   
   
   
   
   
   
   
4. Repeat the process with the Enter New Sample button until all samples are create in the sample set:
   
   
   
   
   
   
5. Click the Save Sample Set button to save the sample set.
   
   
   
   IMPORTANT : If you do not save the sample set, the sample information and the sample set are lost. ( If you return to the Sample Sets page with the same browser type in a short period of time (within a few hours), your sample information might still be available and you might be available to save it then.)

Import a CSV file of sample information

You can define samples with a comma-separated (CSV) file of sample information. This file contains only samples information, without anything about the sample set itself. The CSV file can have either the .csv or .txt file extension.

You can create a new sample set that contains your new samples or add these samples to an existing sample set.

Follow these instructions to import your CSV file:

1. In the Plan > Samples tab, click the Import Samples from File button:
   
   
   
   
   
   
   
   
2. The Import Samples page opens:
   
   
3. In Step 1, click the Select File button and browse to the file with your sample information.
   
   
   
   
4. In Step 2, either select an existing sample set to add these new samples to, or click Add Sample Set... to create a new sample set.
   
   
   
   
5. If you click Add Sample Set... , a new sample set area opens:
   
   
   1. Enter the name of your new sample set and a meaningful description for it.
   2. In the Group Type menu, select the relationship type that describes your samples. Or select Other if your CSV file mixes samples of different relationship types.

6. Click the Save&Finish button.

Example CSV file contents

Example 1

Sample Name (required),Sample ID,Gender,Type,Group,Description

SampleA,A123456,Male,Father,1,vague description

SampleB,B123456,Male,Self,1,vague description

SampleC,C123456,Female,Mother,1,vague description

SampleD,D123456,Female,Self,3,

Example 1 defines a trio of related samples and another unrelated sample.

Sample D does not have a description, but the comma for the description field is required.

Example 2

Sample Name (required),Sample ID,Gender,Type,Group,Description,Freezer

SampleA,A123456,Male,Self,0,vague description,freezer1

SampleB,B123456,Male,Self,1,vague description,,

SampleC,C123456,Female,Self,2,vague description,,

Example 2 shows the use of a custom attribute named Freezer. The two samples that do have the Freezer attribute included still need a comma for the attribute field.

Edit a sample set

You can edit a sample set from the Sample Sets tag (Plan > Samples). Click the gear menu for the sample set:

In the Edit Sample Set popup, you can change the sample set name, the group type (which is the Ion Reporter Software relationship type), and the sample set description:

Edit a sample

To edit a sample, click the expansion arrow to the left of the sample set to open the sample list:

Then click the gear menu for the individual sample:

The Edit Sample in Set option to edit the sample information.

Vocabulary and field restrictions

When sample sets are used to automate integration with Ion Reporter Software, the sample information must follow the rules for Ion Reporter Software samples.

Sample relationships and group number

The following sample relationships are supported:

• Self
• Tumor, Normal
• Control, Sample
• Father, Mother, Self

Each group number in a sample set can only be used for one of the above combinations.

Notes:

• "Self" is used both for a single sample and for the Proband sample in a trio relationship. "Self" in a trio relationship is converted to "Proband" in a run plan.
• A single sample is not related to other samples and is analyzed by itself.

Gender

Always supply a value for a sample's gender. Select Unknown if the gender is not known.

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