Aligning unmapped reads to viral genomes

Question

[cristina_sabiers]

I found this tutorial pretty interesting, so I put the link to share :)

http://www.cureffi.org/2013/01/25/aligning-unmapped-reads-to-viral-genomes/

Thanks at god didn't need to have a heavy pc to be able to do it (I just crashed my head with the code...and make work Phyton...)...so I got my unmmaped reads, pretty interesting get herpesvirus on first place (was suppose to be like that) and curiosity Variola appears in second place. Sadly cant do this with RNA virus like hepatitis C, for that if I'm not wrong I need RNA seq

Well I'm just curious, someone has seen the infected virus on top of the list from an individual with a know disease like for sample HIV and isn't with ARV medication? Isn't any place where I could down a bam file from an known infected individual???

I found another interesting program like Virus Finder, this one seek for virus into the genome if Im not wrong, but can take around 3 day...with my pc probably one week ;_; Has someone try it? I will do when finish with my SNP calling, will take a while XD

(sorry for my bad english)

[GenoMax]

Be careful about drawing conclusions from presence of viral hits in human data (our genome is littered with remnants of various viruses):

RNA-Seq: can one implicate viruses if unmapped reads map to virus sequences?
Plant viruses sequences are found in human brain Rna-seq sample: how to evaluate it?
http://www.sciencedirect.com/science/article/pii/S0888754314001517

[cristina_sabiers]

thanks for the links, I read them... :)))

Anyhow I think must be interesting to get the exome from someone you know is already infected by a virus like VIH(with no ARV treatment) and see if is any significant difference between the others alignments or not...

I don't get like real conclusion :p just tell what I see, hope someone share a bit too...cant do when I have only 15 individuals bam files. I had read from another users if follow the tutorial that I linked before, you find out on first place of alignment score herpesvirus, and in my cases is like that :) Hope later can work with Virusfinder and see (I'm quiet curious about it)...

Thanks!!