Combining viral and host GTF files
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7.3 years ago

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 • 2.8k views
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Thanks. It worked for me.

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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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7.3 years ago

cat host.gtf virus.gtf > host_virus.gtf

use this in htseq_count

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7.3 years ago
e.rempel ★ 1.1k

Hi,

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

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