Viral integration studies using RNA-seq data

Question

[KVC_bioinfo]

Hello,

I am trying to understand how a typical pipeline for analysis of viral integration in RNA-seq data will look like. I understand that is possible to analyze in DNA-Seq. However, in RNA-seq data the introns are spliced out.

So, let's say the viral integration occurred in intron and it is spliced out. How we will study that when we have RNA-seq data.

I am referring to this pipeline. Are they making the assumption that all the viral integration is occurring only in the exonic region?

[VHahaut]

Just a possibility since most insertion sites from their RNA-seq are in intronic or intergenic regions: Not all introns are spliced so they might still find some insertions sites from them (with less probability). The same reasoning should work for intergenic regions that are sometimes translated. However if the sequence is spliced I don't see how they could infer the presence of the virus.