UNDER CONSTRUCTION
Introduction
UCSC genome bioinformatics supports mammalian, insect, fish, avian, and some fungal genomes.
IGBQuickLoad contains genome directories with sequence and annotations data for some (not all) genome assemblies supported at UCSC.
The following describes how to add a new genome version to the IGB QuickLoad repository and update IGB synonyms.txt.
Command-line utilities you'll need need
- faToTwoBit from UCSC
- twoBitInfo from UCSC
- UNIX wget (not installed by default on Mac but available on most other UNIX systems)
- UNIX sort (should be pre-installed on any UNIX system, including Mac)
Install these in a directory in your PATH.
If you're doing this on a Mac desktop or laptop computer, 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 the following to ensure that the shell can find the programs.
export PATH=.:$HOME/bin:$PATH
Step-by-step guide to adding a new UCSC genome to IGBQuickLoad
Get the QuickLoad data repo
Check out or update a copy of IGB QuickLoad data and source code directories.
$ svn co https://svn.transvar.org/repos/genomes/trunk/pub/quickload
If you already have a copy, just update using svn up.
Open a Web browser and find the genome you would like to add in the Table Browser at UCSC
Go to http://genome.ucsc.edu/cgi-bin/hgTables