Viral gene in data

[friddy]

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?

[GenoMax]

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.

[friddy]

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?

[GenoMax]

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

[friddy]

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