Viral integration analysis

Question

[KVC_bioinfo]

Hello,

I am looking into viral integration in RNA-seq data (human samples). I came across two pipelines VirusFinder and VirusClip both of them claim that they can deal with RNA-seq data however both of them do not use a spliced aware aligner for the alignment.

I am very confused how does that work? Can someone help me with this regard?

Thank you

Answer 1

[ATpoint]

From the VirusClip paper (figure1) they say that they align the reads to the virus genome, not to the host transcriptome. Therefore, no splice-aware aligner is required.

[KVC_bioinfo]

Thank you. I read the manual again and now makes more sense to me.

Also, what is the input file for ANNOVAR in VirusClip?