Combining viral and host GTF files

Question

[divya.nandakumar]

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!

Answer 1

[Nicolas Rosewick]

cat host.gtf virus.gtf > host_virus.gtf

use this in htseq_count

[divya.nandakumar]

Thanks. It worked for me.

[GenoMax]

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.

Answer 2

[e.rempel]

Hi,

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