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Introduction
The following instructions assumes you are not going to make a new genome version directory and that all you need to do is update RefGen, mRNA, and EST files.
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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.
For genomes harvested from UCSC, this foundation gene annotations data typically are from the the UCSC refGene table. If a genome does not have a refGene table, we instead use ensGene or whatever other genes data set looks the most complete and the most useful.
Tools you need
- tabix from samtools sourceforge site
- bgzip from samtools sourceforge site
- UNIX wget (not installed by default on Mac but available on most other UNIX systems)
- UNIX sort
- UNIX gunzip
Install these in a directory in your PATH.
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If you're doing this on a Mac desktop or laptop computer, best practice is to create a directory called "bin" in your home directory and save all compiled binaries there. Edit your .bash_profile file to include a line like:
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export PATH=.:$HOME/bin:$PATH Then save all your downloaded or compiled programs (like tabix, bgzip, wget) to bin in your home directory |
How to guide
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Step-by-step guide to updating UCSC data sets in IGB QuickLoad
Get the QuickLoad data repo
Check out or update a copy of IGB QuickLoad data and source code directories.
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