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Old 02-11-2016, 02:39 AM   #1
friddy
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Red face 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?
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Old 02-11-2016, 05:58 AM   #2
GenoMax
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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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Old 02-11-2016, 06:06 AM   #3
friddy
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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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Old 02-11-2016, 06:17 AM   #4
GenoMax
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You would use the gtf file when you get read counts for the genes.
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Old 02-11-2016, 06:24 AM   #5
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Ok, I was planning to use kallisto to get the counts..
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human genome, kallisto, rna-seq aligners, viral genome

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