RNAseq how to map Mouse+Virus Genome with STAR

Question

[cook.675]

I have Fasta and GTF files from the mouse and virus genome I would like to map to. From what I have read its best to combine the Fasta and GTF files but I'm not sure how this is accomplished. For instance, would I just cut and past the viral genome directly after the last nucleotide of the mouse genome fasta?

If that's correct then I would need to determine and change all the positions of the genes in the Virus GTF file before combining them right? Then would I just cut and past the viral gene annotations from the GTF to the end of the mouse GTF (and only use 1 header)

I read its possible to input two fasta files into STAR and one GTF that has all the annotations. Can I do it this way and just paste the annotations from the virus GTF into the mouse GTF? How to deal with the nucleotide gene positions from the virus Gif if doing it this way?

Thanks for any help you could provide!

Answer 1

[GenoMax]

You can simply cat host.fa virus.fa > hybrid.fa. Then index this file with STAR. Depending on whether your GTF's have the same format the viral annotations could be appended to the end of mouse GTF in same manner.

Viral identifiers would be treated as extra "chromosomes" in this case.

[cook.675]

Thanks so much, would I need to delete the headers at the top of the viral files, for instance the....

>NC_001846.1 Murine hepatitis virus strain MHV-A59 C12 mutant, complete genome

At the top of the virus fasta?

[GenoMax]

No that actually would become an "extra" chromosome name when appended to genome fasta. You will use that to identify the reads that map to the particular reference. It should match what is in your GTF. If your GTF contains NC_001846.1 then remove the remaining descriptive part.

Answer 2

[swbarnes2]

Your mouse genome is already a multi fasta, with each chromosome being its own header + sequence. The virus can just be catted onto the end like another chromosome with header + sequence.