Introduction

ExonViz is a simple tool to generate and draw transcripts that include coding and non-coding regions. All exons are to scale and the reading frames of the exons are visible. Single or multiple variants along the transcript can be drawn and will automatically be shown in the correct location. Further, we allow the user to generate their own transcripts to incorporate features like poison or cryptic exons. ExonViz can be accessed as a web-application via exonviz.rnatherapy.nl, and is also available as a python package from PyPI. The source code is available on github.

How it works

The transcript specified by the user, including any variants, is retrieved using Mutalyzer, and all relevant information such as coding region and exon sizes are extracted. When using the command line version of ExonViz, it is also possible to specify custom transcripts.

If the user specifies a gene name, the corresponding MANE Select transcript will automatically be selected. If there are multiple MANE Select transcripts defined for a gene, the first transcript will be used. ExonViz uses MANE Select release 1.2.

To indicate the difference between the coding and non-coding regions of the transcript, the non-coding regions is drawn at half the hight of the coding region.

The start and end phase of coding exons are indicated using notches and arrows. If the end of the exon coincides with the codon boundary (phase 0), the exon end is drawn straight.

Variants are drawn inside the correct exon, and a legend is shown at the bottom of the figure. By default, ExonViz will cycle through the same five colors for the variants, but this can be specified by the user. If the same name and color is used for multiple variants, they will only be shown once in the legend. This can be useful when there are many variants, and the color is based on e.g. the pathogenicity of the variants.

Settings

scale

The scale of the drawing determines how many pixels are used per basepair of the transcript. The default scale is 1:1, which means that an exon of 100bp will be drawn 100 pixels long.

height

The height of the drawing determines how high each exon is drawn, and also determines the size of the notches and arrows (0.25 * height, to be exact).

Because we need a certain amount of space to draw the notches and arrows, some transcripts cannot be drawn at the default scale and height. For example, transcript ENST00000621218.5 of PLP1 must be drawn at a scale of at least 1.3 with the default height, because only the very last few basepairs of the first exons are coding.

width

The width determines the maximum width of the figure. ExonViz guarantees that the figure will not go over this limit. It will try to distribute the exons in such a way that every row of the figure is filled. Sometimes, an exon will be split over multiple rows to ensure they fit. If this happens, the name of the exon (usually its number) will be shown for every split of the exon.

The legend will also be split over multiple rows, unless the variant name is so long that it will not fit on the page by itself. If this is the case, ExonViz will display an error.

When using the command line version, the names of both variants and exons can be modified.

noncoding

By default, the non-coding regions of the transcript are not show, but this can be changed using the noncoding option.

gap

gap determines the gap between exons when they are drawn on the same row.

color

color determines the color of the exons. When using the command line version, the color of individual exons can be set.

exonnumber

Set the name of the exons to their number. By default, exons have no name. When using the command line version, the name of each exon can be customised.

firstexon and lastexon

These two options can be used to only draw a subset of the specified transcript, which can be useful for very large genes.

variantcolors

This option determines the list of colors that ExonViz will cycle through for the specified variants.

–dump-exons and –dump-variants

Use these two flags to write the exons and variants to the specified files. This allows the user to modify the retrieved transcript in a simple spreadsheet program, and later draw the modified transcript. These option are only available for the command line version.

–exon-tsv and –variant-tsv

Rather than query Mutalyzer for the transcript information, read the exons and variants from the specified tsv files. These option are only available for the command line version.