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Viral integration analysis

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

virusfinder rna-seq virus-clip
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updated by Ram Ram • written by KVC_bioinfo KVC_bioinfo

1 answer

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.

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written by ATpoint ATpoint

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

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

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written by KVC_bioinfo KVC_bioinfo

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