GWIPS-viz: User Guide


Getting Started
Browser Window

Getting Started: GWIPS-viz gateway

If you are unfamiliar with the UCSC Genome Browser, you might like to visit OpenHelix where very nice tutorial and training materials on the UCSC Genome Browser are provided.
Otherwise, the instructions below may be sufficient for using GWIPS-viz.

1. Select the genome from the Represented Species list or click one of the icons at the top of the page.
2. Select the genome assembly from the assembly dropdown menu.
3. Enter a position on the genome in the format chromosome:start_position-end_position, or a search term such as a gene name or transcript ID and click GO .

Browser Window

1. The GWIPS-viz Genome Browser page consists of a main central window pane with a white background in which the data is displayed.
    Data is displayed in the form of one or more tracks which are stacked vertically within the main window.
2. By default the Global aggregate track from the Elongating Ribosomes (A-site) track group is displayed for each genome.
    This track is coloured red except for bacterial genomes where strand orientation is used and reads aligning to the forward strand are red and reads aligning to the reverse strand are blue.
    To display the subtracks of the Global aggregate track, or any of the individual study tracks, click on study link in the track group panel to get to the track settings page.
    In the track settings page, tick the checkbox(es) for the individual subtracks. Set the Display mode dropdown to Full and click Submit.
    The GWIPS-viz Genome Browser page should now display the selected individual tracks.
3. By default the Gobal aggregate for mRNA-seq data is also displayed. This track is coloured green for all genomes except bacteria where the mRNA-seq reads are coloured similarly to the Ribo-seq reads.
4. Depending on the selected genome, there will be one or more gene annotation tracks displayed. In the figure the RefSeq gene annotations for human are displayed in blue.
    The Annotation Tracks and External Data track group contains other useful tracks such as conservation tracks, repeat annotations etc.
5. Above and below the main window, a number of button options exist for navigation and display configuration. Use these buttons to navigate to different areas of the genome.

Table Browser And Sessions

Detailed help pages are available for bot the Table Browser and User Sessions