Viral integration

[oghzzang]

Dear MAVIS team.

Hi I'm Oh.

I have two questions.
Q1. If I change reference or annotated files, can I visualize viral integrations?

Q2. I found the following fusion. (the Promoter of TP53 gene: coding region of CTNNB1 gene)
But, in this case, the picture is not drawn with the default option.
Is there a way to draw even if one partner is in non-coding region?

Many thanks

[creisle]

Hi Oh,

Sorry for the slow response.

Q1. If I change reference or annotated files, can I visualize viral integrations?

You will be able to visualize any fusion proteins should you include a "chromosome" for the viral sequence in the reference and the viral genes in the annotations file

Q2. I found the following fusion. (the Promoter of TP53 gene: coding region of CTNNB1 gene). But, in this case, the picture is not drawn with the default option. Is there a way to draw even if one partner is in non-coding region?

The visualizations are primarily intended to display gene-gene fusions so drawing of synonymous or intergenic fusions is off by default, however if you set the following both to False you will produce all drawings

https://mavis.readthedocs.io/en/latest/configuration/settings/#draw_fusions_only
https://mavis.readthedocs.io/en/latest/configuration/settings/#draw_non_synonymous_cdna_only

Hope that helps!