Viewing novel exon junctions in the genome browser

From Array Suite Wiki

A tutorial for getting started with the Genome Browser is located here. This page specifies helpful settings for the use case of viewing novel exon junctions in the Genome Browser.

Genome Browser Settings

Hover over the track name to see some general options for Genome Browser viewing. To look at known or novel exon junctions, you will need to enable the display of this data, as it is hidden by default. Hover over the track name, click "Apply to all tracks" and select the Show Exon Junctions option.


You can further filter the displayed data that is being streamed from the BAM file to show only identified exon junctions (known and novel). To enable this, right-click on the alignment track and select "Filter Alignments". Click on the "Exon Junction Reads Only" option to enable this filter.


Alignment Track Settings

Some specific settings for novel exon junctions in the alignment track menu can be edited to better identify novel exon junctions Track_Properties_Alignment_Track.txt#Exon_Junctions. Right click on the alignment track and select "Set track properties", then highlight all tracks you would like to edit. These settings are most useful:

  1. Minimal Count for any exon junctions - this can be lowered to 1 to view all identified novel exon junctions.
  2. Novel Exon Junction Color - can be edited to visually identify novel exon junctions, as opposed to known junctions.



For more information on alignment track settings, please see Track_Properties_Alignment_Track.txt