How to find an inserted human gene in Drosophila RNA-seq data

Question

[williamsbrian5064]

I am working on a collaboration and we recently generated some RNA-seq data. So the lab that we are working with inserted a human gene into the Drosophila genome to see the effects of a specific mutation. They were able to insert the gene and did some RNA sequencing. I was given the task of working with the RNA-seq data but I have no idea how to find this gene that was inserted. I've worked with RNA-seq data in the past but never like this. How an I suppose to find the gene? I know there are programs out there to find novel isoforms found in RNA-seq data but what do you do when you're looking for an entire gene.

I thought about trying to somehow add the human gene into the Drosophila index? but the index is very specific about gene location right?

I think this is an easy question but I'm not sure where to begin here. Any help would be amazing.

Thanks!

[GenoMax]

Just add sequence of human gene to the drosophila genome as a new "chromosome" and analyze as before. You will have to re-create your own aligner indexes with this modified genome.

[williamsbrian5064]

How would I go about doing that? I'm not sure how to alter the transcript fasta file to do that?

[GenoMax]

Put your human gene sequence in fasta format in a file. Do cat transcript.fa human.fa > mod_transcript.fa. Build indexes using mod_transcript.fa file.

If you just want to see if there are reads expressed from the human gene then you could do something like this, using bbduk.sh from BBMap.

bbduk.sh in=data.fq.gz outm=matched.fq.gz outu=non_matched.fq.gz k=31 ref=human.fa

Reads going into file matched.fq.gz will be for human gene.

[williamsbrian5064]

I will give that a try! Thanks for the help