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Introduction
An IGB user contacted us with a request to add a new genome to the IGB QuickLoad system - the Xenopus tropicalis genome assembly dated November, 2009, also called JGI 4.2/xenTro3. (See: http://genome.ucsc.edu/cgi-bin/hgGateway?hgsid=262072157&clade=vertebrate&org=X.+tropicalis&db=0).
Because this genome is supported at the UCSC Genome Browser, adding it to the system should be fairly straightforward. All we need to do is download the data, format it, and move it onto the main IGB QuickLoad site currently hosted at UNC Charlotte, in the Bioinformatics and Genomics Department's server room.
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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. |
Methods
Downloading sequence data (2bit file) from UCSC Genome Bioinformatics
Step one is to download the sequence data.
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$ svn add X_tropicalis_Nov_2009.2bit Transmitting file data . |
Creating genome.txt using twoBitInfo
Next, I used twoBitInfo to make a "genome.txt" file reporting the names of the assembled chromosomes and contigs and their sizes:
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$ svn ci genome.txt -m "Output from twoBitInfo on current version of X_tropicalis_Nov_2009.2bit" |
Downloading genome annotations (ESTs and RefSeq genes) from UCSC Table Browser
My plan (currently) is to get the RefSeq genes track from UCSC and deploy it on our QuickLoad site. I'll provide meta-data about the data set using the annots.xml file. (More on this later.)
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I also checked the ESTs data set. There are around 1.5 million ESTs for Xenopus. I'll download that data set as well, but set it up so that users can access it on a region-by-region basis by sorting and indexing using the tabix utility. I'll also need to massage the format a bit to get it to make the PSL (blat output) format.
Processing ESTs using tabix to support fast access in IGB
To process the EST data set, I used the following command to strip off the first column
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Next, I added each of the data files to IGB QuickLoad subversion repository - the sorted, bgzip-compressed EST data file, its index file, a compressed (gzip) file for the RefGene data set, and a compressed, gzip'd file for the mRNA data set. Since both will be loaded as soon as the user visits the genome version, I did not bother to make tabix'd versions of those files.
Deploying the files on QuickLoad
I've created a number of data files, and so my next step will be to try opening them in IGB. I also want to test whether IGB will be able to open and display the genome sequence.
So my next step is to create an annots.xml file IGB will use to get a listing of the annotations available for this genome as well as styling information, e.g., the background colors to use for gene annotations, whether to load all the annotations immediately, and so on.
Creating new annots.xml file for Xenopus genome and annotations
Being a bit lazy, I usually just copy and paste another annots.xml file from another part of the repository when setting up a new genome. I use svn for this, however:
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The "max_depth" parameter refers to the maximum number of overlapping annotations that can appear in a stack within a track. The "name_size" parameter specifies the font size for the track labels that appear on the left-hand side of the main display menu. The "url" parameter specifies where IGB links to when the user clicks the info button (blue "i" icon) next to a data set. In this case, we link back to the main UCSC Web page, since this is where the data came from originally. The "name" parameter indicates the file name IGB should load, and the "description" parameter specifies the tooltip text that will appear when the user hovers the mouse over the data set in the Data Access Panel. The "title" specifies the name of the data set as it will appear to the user.
Testing new genome version directory in IGB
Finally, I added my local QuickLoad site to IGB (using the Configure link in the Data Access panel) and loaded up the new genome.
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My last step was to log into the main IGB QuickLoad site and run "svn up" to deploy the new genome and all its associated data files on the main site to ensure that all IGB users can now access the data.
Conclusion
All in all, the entire process, subtracted breaks for lunch and meetings, took about four hours, including the time it took to write this tutorial.
Visualization of the newly added genome
Here is what the genome will look like for some-one visiting this genome version for the first time:
