IGB Developer's Guide
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Table of Contents

Introduction

The main IGB QuickLoad site is configured so the canonical gene models annotations are loaded into IGB as soon as the user selects the corresponding genome version. This is configured through the `annotsannots.xml` xml file that resides in every genome version directory. Any data set with attribute "load_model" set to "Whole Genome" will automatically load into IGB.

For many genome versions, the canonical gene models are provided by UCSC Genome Bioinformatics from their refGene data collection. These get This refGene collection gets updated from time to time, and so it is important for users that we keep these in sync with what is shown update the main IGB Quickload site when UCSC updates their data. This ensures that what users see in IGB matches what they see in the UCSC Genome Browser software.   
The following instructions explain how to update this file. The instructions assume you are not going to make a new genome version directory and that all you need to do is update a refGene data set.

For many genomes supported by UCSC, the refGene data collection from UCSC represent the canonical gene model annotations for that genome. 

 

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Understand IGB QuickLoad naming conventions

Note

IGB QuickLoad file names should include the genome version and the UCSC table name. The title in the annots.xml file should match the track name but should not include the species name, as that will be obvious to the user and may make linkout patterns harder to maintain.

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