Question: Combining viral and host GTF files
0
gravatar for divya.nandakumar
17 months ago by
divya.nandakumar20 wrote:

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!

sequencing rna-seq alignment • 727 views
ADD COMMENTlink modified 17 months ago • written 17 months ago by divya.nandakumar20

Thanks. It worked for me.

ADD REPLYlink written 17 months ago by divya.nandakumar20

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.

ADD REPLYlink written 17 months ago by genomax59k
3
gravatar for Nicolas Rosewick
17 months ago by
Belgium, Brussels
Nicolas Rosewick7.0k wrote:

cat host.gtf virus.gtf > host_virus.gtf

use this in htseq_count

ADD COMMENTlink written 17 months ago by Nicolas Rosewick7.0k
2
gravatar for e.rempel
17 months ago by
e.rempel710
Germany, Heidelberg, COS
e.rempel710 wrote:

Hi,

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

ADD COMMENTlink written 17 months ago by e.rempel710
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