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Introduction
The following instructions assume you are not going to make a new genome version directory and that all you need to do is update refGene, all_mrna and all_est files.IGB QuickLoad is configured so that a set of foundation gene annotations (gene models) load 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 This is configured through the annots.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.
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As of IGB 10.1.0 most UCSC genome versions and tracks should now be available by default in IGB via the UCSC REST data provider. |
Understand IGB QuickLoad naming conventions
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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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However, the UCSC genome browser sometimes include species names in the title of its mRNA track. IGB QuickLoad data sets should not include species names in the titles. For example, the title of an mRNA track is always "mRNA" and never (for example) "Zebrafish mRNA."
Command-line utilities you'll
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need
- tabix and bgzip from htslib
- git
- svn
- UNIX wget (not installed by default on Mac but available on most other UNIX systems)
- UNIX sort
- UNIX gunzip
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export PATH=.:$HOME/bin:$PATH |
Step-by-step guide to updating UCSC RefGene data
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set in IGB QuickLoad
Get the QuickLoad data repo
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$ git clone https://bitbucket.org/lorainelab/genomesrcgenomesource |
If you already have a copy, then update it. Changed into your local copy and run:
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$ git pull origin mastermain-JDK8 |
Use svn to get a copy of the QuickLoad data repository: TO BE UPDATED
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If you already have a copy, just update using svn up. Change into your checked-out, local copy and run:
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$ svn up |
Add
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quickloadsource to your PATH (to run the python code there)
Add quickloadsrc quickloadsource to your PATH as it contains a python script you'll use to created BED detail files from ordinary BED files. Edit the .bash_profile file as in above:
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export PATH=.:$HOME/quickload_srcquickloadsource:$HOME/bin:$PATH |
Pick a genome to update and change into the genome version directory
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Use ucscToBedDetail.py (from https://bitbucket.org/lorainelab/genomes_srcgenomesource) to create a new BED file with gene symbol and description
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