Torrent Suite SoftwareAdministration Guide

Torrent Suite Software space on Ion Community

Administration Guide TOC

Configure Basecaller Default Parameters

This section describes how to use the Admin Interface to change the basecaller default parameters, which include the quality trimming parameters .

Each chip type has a separate basecaller parameter field. The basecaller parameters and quality trimming parameters can be customized for each chip type.

The quality and trimming parameters are described in this table:

Note : Basecaller arguments by default are different for sequencer type, regular analyses, thumbnail analysis, and recalibration. This example shows the Basecaller arguments for regular analyses on Ion PGM data.

Follow these steps to change or customize basecaller parameters:

1. In the Rundb administration page, select Analysis Args :
   
   
   
   
   
   
   
   
2. In the Name column, click on the name for your chip type:
   
   
   
   
   
   
   
   
3. Make your basecaller parameter and quality parameter changes to the Default Basecaller args: field:
   
   
   
   ( Note: Enter the basecaller arguments in one line. The example here is wrapped.)
   
   
   
   
4. Click Save .
   
   
   
   
5. Repeat your changes to other chip types also, if required.
   
   
   
   

More information on quality trimming is available in the Technical Note - Filtering and Trimming in the installed product docs or on the Ion Community at http://ioncommunity.lifetechnologies.com/docs/DOC-6637 .

Adapter trimming is described in the section Removal of Adapter Sequence.

Quality trimming is described in the section Removal of lower-quality 3' Ends with Low Quality Scores.