How to Visualize Data in the Genome Browser

Visualizing data in the genome browser

The genome browser currently supports visualizations for mouse and human BigWig and BED files. 

Prior to visualizing data in the the genome browser you must set up your library and upload data.

Files can be uploaded directly to the library or you can upload FASTQ files and build a pipeline to process them using Bowtie2 and MACS2.  Once your files have been uploaded to the platform or generated by running a pipeline you can begin visualizing your data in the IGV genome browser. 

Step 1:  Accessing the Genome Browser 

Go to your workspace and create a project. Within the project create an analysis and select "Genome Browser", you will be prompted to select the reference genome you would like to work with. 

Step 2:  Use the top tool bar to specify the tracks you would like to work with in the genome browser.  

  • Genome : Reference genome. 
  • Tracks: Select from a list of publicly available tracks. 
  • Experiments: Choose between publicly available experiments from ENCODE and/or experiments from your library.  Select the type of experiment you would like to work with. From here you will see a list of experiments that are currently in your library or available from ENCODE. Under each experiment are the files associated with it, you can add any BigWig or BED file to the genome browser.

Working with publicly available Experiments

  • Select Experiments> ENCODE> and explore ChIP or ATAC experiments. 
  • Click on the accession  under the "derived from" column to see the metadata associated with the sample.
  • If working with ChIP experiments, filter the experiments by searching for a specific ChIP target. 

Step 3: Explore the genome browser for observations.

Use the drop down menu to navigate to a specific chromosome, search for a specific gene or chromosomal coordinates. Use the plus ad minus button to zoom in and out to specific regions in the chromosome, you can also left click and drag to navigate. Click on a specific region to display the position and value in the right hand panel. 

Use the settings gear next to a track to customize track name, height, colour, density and visibility.

Step 4: Explore genes and multi- omic observations.

Learn more about genes and view observations across all datasets you have uploaded or generated on the platform. Select the name of a gene under the "GeneCode V40" track and this will open a gene card  on the right hand side of the application. Clicking on "Detailed View" at the bottom of the card  will enable you to explore the following

  • All of the gene sets the gene is involved according to EnrichR and Reactome 
  • Associated papers describing a reference into function 
  • All of the observations you have on the gene in all datasets you have uploaded to or generated on the BIoBox platform. 
  • A gene network map displaying all of the interactions the gene has with neighbouring genes and the nature of their relationships 
  • Disease related information if the gene causes or is correlated to any diseases. 

Using the "Save SVG"  button located at the top of the genome browser you can export an SVG image of your genome browser session. Genome Browser Sessions will not save so please ensure you save the necessary images from your analysis.