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  • Viral gene in data

    hi,

    I have some RNA-seq data for human cell line samples and one of them expresses a viral gene, I would like to map and quantify the data with Kallisto and I'm thinking if I could just add the viral genome sequence to my human reference sequence and map all my samples to that?

  • #2
    That should be ok as long as you check if reads multi-map to the virus/genome. You would need to add a corresponding annotation entry to your GTF files to get counts.

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    • #3
      Thanks, what I have tried now is to build an index from a combined fasta file, where in the process should I use gtf files?

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      • #4
        You would use the gtf file when you get read counts for the genes.

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        • #5
          Ok, I was planning to use kallisto to get the counts..

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