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Combining viral and host GTF files

Hi,

I have RNA-Seq data from virus infected cell. I would like to get the counts for both viral and host transcripts. I added the virus fasta sequence to the human genome as an additional "chromosome" so that I could align to both the viral and human DNA at the same time. But I don't know how to combine the GTF files to get the counts for both. I used htSeq count independently with the viral and human GTF files to get the counts for each separately. But I was wondering if there is a way to use a joint GTF file. I would appreciate any help!

rna-seq sequencing alignment
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updated by Biostar Biostar • written by divya.nandakumar • divya.nandakumar

2 answers

cat host.gtf virus.gtf > host_virus.gtf

use this in htseq_count

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written by Nicolas Rosewick Nicolas Rosewick

Please accept (use the green checkmark) against the answer that worked to provide closure to this thread. If both answers worked then you can do this for both.

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written by GenoMax GenoMax

Hi,

I think you could just add the viral GTF to the human assuming the chromosome identifiers don't overlap.

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written by e.rempel e.rempel

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