Sashimi tracks

Analysis of mRNA isoform expression is a key aspect of understanding gene expression. For many genes, the change in isoform ratios for a given gene produce a more significant physiological effect than the overall expression level of that gene. Isoforms are typically visualized as Sashimi plots, a way of quantitatively visualizing splice junctions for mRNA sequences aligned to an annotated genomic reference. Sashimi plots allow you to screen differentially spliced exons in genomic regions of interest. If data are available, you can choose to display a Sashimi track in the Analysis view.

For detailed information about applying tracks, see Work with Tracks. This is the Track panel item to check if you wish to display a Sashimi plot:

When the Sashimi track is visible in the Analysis view, it consists of two components:

• A bar graph showing the abundance of each exon

• Arcs representing the number of reads split across the junction, also referred to as “junction depth.”

Multiple Sashimi plots from multiple samples can be displayed simultaneously.

Scroll to the bottom of this page to see two videos showing Sashimi tracks in action.

Sashimi track data can come from the sequences in an assembly, or can be imported separately using File > Add Track. When data are available for a given sample, GenVision Pro automatically replaces the Coverage track with a Sashimi plot, which contains the same Coverage histogram, but also allows for “arcs” to be displayed. The number at the top of each arc represents the number of split reads; the thickness of each arc is proportional to this number. Note that split reads do not necessarily correspond to introns; other types of structural variation can also cause SeqMan NGen to split reads. Annotations are not considered when creating the Sashimi track.

For a brief video showing RNA-Seq data analysis using the Sashimi track, see the second video in Launch a session from within ArrayStar.

To change Sashimi track options:

To learn how to access the options section for this track, see Options section.

• By default, Sashimi graphs have navy blue arcs and purple coverage histograms. To choose different colors, click on the Arc color and/or Coverage color box and make a selection from a color chart.

• By default, arc numbers (“labels”) and the Sashimi plot, as a whole, do not have background colors. To add colors, check Label background color and/or Background color, then click on the corresponding color box and make a selection from a color chart. To turn the colors off again, uncheck either or both check-boxes.

• Minimum read count lets you set a threshold for the minimum number of split reads needed to display an arc. If this value is set to zero, no filtering will occur.

• Maximum span allows you to set a threshold for the maximum allowable arc length, in bases. To turn off this filter, delete any numbers from the text box, leaving it blank.

• Under Coverage y-axis, set a Maximum limit for the height of the y-axis on the coverage graph. This setting is equivalent to the Y-axis range maximum in the Numeric track options.

Click if you wish to return to the default values.

*Note: The height of track labels is specified using the presentation Font settings in View > Style > Analysis. To change the height of the graph and the white space surrounding it, use the sliders in the Layout section.

This video shows how to apply and interpret Sashimi plots in GenVision Pro:

This video shows an RNA-Seq workflow that begins with assembly in SeqMan NGen, proceeds to downstream analysis in ArrayStar, and then uses ArrayStar’s Send Selection to GenVision Pro command to open the results in GenVision Pro. Once in GenVision Pro, the Sashimi track is applied. (GenVision Pro section begins at 2:41).