IGB Developer's Guide
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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 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 many genome versions, the canonical gene models are provided by UCSC Genome Bioinformatics from their refGene data collection. This refGene collection gets updated from time to time, and so it is important for users that we 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.


As of IGB 10.1.0 most UCSC genome versions and tracks should now be available via the UCSC REST data provider by default in IGB.


Understand IGB QuickLoad naming conventions

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.

For example, gene models data for the UCSC track named RefSeq Genes is stored in a table called refGene. In IGB QuickLoad, the data file should be named G_species_strain_MMM_YYYY_refGene.bed.gz (a compressed BED detail file) and the title attribute in annots.xml should be RefSeq Genes.

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 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

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 updating UCSC RefGene data set in IGB QuickLoad

Get the QuickLoad data repo

Check out or update a copy of IGB QuickLoad data and source code directories.

Use git to obtain a copy of source code:

$ git clone https://bitbucket.org/lorainelab/genomesource

If you already have a copy, then update it. Changed into your local copy and run:

$ git pull origin main-JDK8

Use svn to get a copy of the QuickLoad data repository: TO BE UPDATED

$ svn co TO BE UPDATED

If you already have a copy, just update using svn up. Change into your checked-out, local copy and run:

$ svn up

Add quickloadsource to your PATH (to run the python code there)

Add 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:

export PATH=.:$HOME/quickloadsource:$HOME/bin:$PATH

Pick a genome to update and change into the genome version directory

Open a Web browser and find the genome in the Table Browser at UCSC

Go to http://genome.ucsc.edu/cgi-bin/hgTables

Update refGene data set

File name: G_species_strain_MMM_YYYY_refGene.gz
Data set title: RefSeq Genes

Get refGene data from UCSC Table Browser

Configure Table Browser

Configure Table Browser with the following settings:

  • choose assembly using release date to match it with IGB QuickLoad genome version
  • choose group: Genes and Gene Prediction Tracks
  • choose track: RefSeq Genes
  • choose table: refGene
  • choose output format: BED - browser extensible data
  • enter output file G_species_MMM_YYYY_refGene.bed.gz
    • The prefix should be THE SAME AS the genome version directory name, with _refGene appended.
  • file type returned: choose gzip compressed

UCSC data set file names saved in IGB QuickLoad should always include the IGB genome version name followed by an underscore character followed by the UCSC table name. The title field in the annots.xml file should always be the UCSC track name because that is what users will recognize from having used the UCSC genome browser.

Click the "get output" button to download the data

Get gene info and accession info files from NCBI ftp site

$ wget ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/gene2accession.gz
$ wget ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/gene_info.gz

Create BED detail file with gene information

Use ucscToBedDetail.py (from https://bitbucket.org/lorainelab/genomesource) to create a new BED file with gene symbol and description

For example, do something like this:

$ ucscToBedDetail.py ~/Downloads/G_species_MMM_YYYY_refGene.bed.gz G_species_MMM_YYYY_refGene.bed

This will create a new BED detail file (G_species_MMM_YYYY_refGene.bed) in the current working directory.

Note that for this to work, gene2accession.gz and gene_info.gz must be in your current working directory.

You can also provide these files using options -a and -g if you have saved them to a different location. See the script documentation for details.

Sort, compress, and index

$ sort -k1,1 -k2,2n G_species_MMM_YYYY_refGene.bed | bgzip > G_species_MMM_YYYY_refGene.bed.gz
$ tabix -s 1 -b 2 -e 3 bed G_species_MMM_YYYY_refGene.bed.gz

Validate the file

Check that it has data

$ gunzip -c G_species_MMM_YYYY_refGene.bed.gz | wc -l

The wc command should print the number of lines in the file, which should be equal to the number of rows in the corresponding refGene table. To find out how many rows the refGene table contains, click \"describe table scheme\" in the Table Browser.

Try to open it in IGB

Open file the file and change load mode to whole genome. Click the genome row in the Current Sequence table. You should see something above every chromosome.

If some chromosomes have no data, go back to the table browser and use the region text area to confirm there was no data for the given chromosome.

Check the chromosomes

Make sure the number of chromosomes listed in the file does not exceed the number of chromosomes listed in the genome descriptor file genome.txt:

$ gunzip -c G_species_MMM_YYYY_refGene.bed.gz | cut -f1 | sort | uniq  wc -l
$ wc -l genome.txt

The first line counts the number of unique sequences appearing the first column of the bed file. The second line counts the number of lines in the genome.txt file.

Edit annots.xml

The annots.xml file description for the refGene annotations contains the date the data were downloaded. Edit the file accordingly to reflect today's date.

Check in the new files

Use svn status command to double-check which files you've changed:

$ svn st

It should print something like:

M  G_species_MMM_YYYY_refGene.bed.gz
M  G_species_MMM_YYYY_refGene.bed.gz.tbi
M  annots.xml

M stands for "modified".

These are the only files that should have changed. If others are different, something has gone wrong.

Check in the files one-by-one:

svn ci G_species_MMM_YYYY_refGene.bed.gz -m "Enter a message here."
svn ci G_species_MMM_YYYY_refGene.bed.gz.tbi -m "Enter a message here."
svn ci annots.xml -m "Enter a message here."
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