References Management Guide

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Torrent Suite Software space on Ion Community

References Management Guide TOC

Manage DNABarcodes and DNABarcode Sets

This section describes how to manage barcode setsin the UI under the References Tab. (For a description of how to use barcodes with an Ion S5, Ion PGM, or Ion Proton Sequencer run, see Use DNA Barcodes with the Ion Sequencers .)

With the pre-installed Ion Torrent barcodes, you can view the barcode sets and the barcodes, incuding the barcode sequences:

View a DNA barcode or barcode set

With your own barcodes sets, you can do the following:

View a DNA barcode or barcode set

Add a custom DNA barcode set

Delete a DNA barcode set

Add a barcode to an existing DNA barcode

Edit or delete an individual barcode

Topics on this page

Access the DNA barcode set pages

You access the barcode sets in the Torrent Browser by clicking the gear menu (near the top right) and clicking the References option:

In the Admin References tab, click the Barcodes option in the left navigation panel:

The DNA Barcodes page opens:

Pre-installed DNAbarcode sets

For pre-installed barcode sets, the following functionality is supported:

• View a DNA barcode or barcode set

The pre-installedDNA barcode sets are seen under the Admin References tab:

View a DNA barcode or barcode set

Follow these steps to view a DNA barcode or barcode set:

1. Click the gear menu, select References , and scroll down tothe DNA Barcodes panel.
   
   
   
   
2. Either click the name of the barcode set to view or click the gear menu Edit option for that barcode.
   
   
   
   

This displays the barcodes in the set:

Note the page number controls to view other pages:

You can click any column header in bold to sort the display by that column.

The Action column gear menu provides Edit and Delete options:

The gear menu Edit option is the same as double-clicking the barcode name.

Dialog buttons are displayed to add a new barcode to this set and to delete the entire barcode set.The barcode edit and delete feature is only for custom barcode sets that you install.

See barcode column table for an explanation of the fields in a DNA barcode.

IonSet1 barcodes

Here are the barcodes in the IonSet1 barcode set:

IonXpress barcodes

Here are the barcodes in the IonXPress barcode set:

IonXpressRNA barcodes

Here are the barcodes in the IonXPressRNA set:

RNA_Barcodes_None barcode

Here is the barcode in the RNA_Barcodes_None barcode set:

Museek_5prime_tag barcode

Here is the barcode in the MuSeek_5prime_tag barcode set:

For custom DNAbarcode sets

For your own barcode sets, you can do the following:

View a DNA barcode or barcode set

Add a custom DNA barcode set

Delete a DNA barcode set

Add a barcode to an existing DNA barcode

Edit or delete an individual barcode

Add a custom DNA barcode set

To add a barcode set, packaged as a list of barcodes in a Comma-separated Variable (CSV) text file, create the CSV file then select the file to add it to the barcode set list.

1. If needed, create the CSV file containing a maximum of 96 barcodes, using Microsoft Office Excel, OpenOffice.org Calc, or an equivalent program. Save the file with a .csv extension.
2. Click the Torrent Browser gear menu (near the top right), select the References option, and scroll down tothe DNA Barcodes panel.Click Add new DNA Barcodes on the right side of the DNA Barcodes panel:
   
   
   
   
3. In the Add New DNA Barcodes dialog, enter the required Barcode Set Name in the edit window and browse to find the Barcode CSV File :
   
   
   
   

4. To view an example CSV file, click Download the example file :
   
   
   
   The example CSV file contains column headers only. The following table describes the column headers:

   Name	Type	Description
   id_str	String	The unique name for this barcode entry.
   sequence	String	The barcode sequence.G, C, A, and T (always upper-case) are allowed.
   adapter	String	The portion of the barcode adapter not used to identify this barcode. Often referred to as the "stuffer sequence". G, C, A, and T (always upper-case) are allowed.
   flow order	--	Not used.
   annotation	--	Not used.

5. Click Upload & Save to add the new barcode set.
   
   
   
   
6. When you return to the DNA Barcodes section, click the Name column header to sort the column and have your new barcode set appear.

Delete a DNA barcode set

This feature is only for your own custom barcode sets.

1. Display the barcode set contents as described in View a DNA barcode or barcode set .
   
   
2. At the top of the page, click Delete Barcode Set . This displays a delete confirmation prompt:
   
   
   
   
   
   
3. Click Yes, Delete! to delete the entire barcode set. Click Cancel to keep the displayed barcodes.

Add a barcode to an existing DNAbarcode set

This feature is only for custom barcode sets that you install.

1. Display the barcode set contents as described in View a DNA barcode or barcode set . Click Add Barcode :
   
   
   
   
   
   
   
   
2. The Add new barcode in set page opens:
   
   
   
   
   
   
   
   Add the barcode informationand click Save Barcode .
   
   See the barcode column table for an explanation of the fields.
   
   The new barcode is added to the set displayed in the current barcode set list.

Delete an individual barcode

The barcode delete feature is only for custom barcode sets that you install.

Follow these steps to remove a single barcode from a custom barcode set:

1. Display the barcode set contents as described in View a DNA barcode or barcode set .
   
   
   
   
2. For the barcode to be deleted, click on the gear menu for that barcode and select Delete :
   
   
   
   
   
   
   
   
3. In the confirmation window, if you are sure, click Yes, Delete! :
   
   

The barcode is removed for the barcode set.

Edit an individual barcode

The barcode edit feature is only for custom barcode sets that you install.

Follow these steps to edit a single barcode in a custom barcode set:

1. Display the barcode set contents as described in View a DNA barcode or barcode set .
2. Click on the ID of a barcode, such as bc03. The Edit barcode in set page opens:
   
   
   
   
   
   
   
   See the barcode column table for an explanation of the fields.
   
   
   
   
3. To edit the barcode details, make your changes and click Save Barcode .

Links to barcode classification pages

• BaseCaller Parameters (including changes in the 4.2 release)
• Troubleshooting Barcode Classification
• Custom Barcode Design
• Filtering and Trimming Tech Note

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