Confirming Viruses detected from NGS data

Question

[Ron]

Hi all,

I found Oncogenic viruses using VirusSeq (http://odin.mdacc.tmc.edu/~xsu1/VirusSeq.html )in some of the RNA-seq HUMAN samples.However I want to view the evidence of these virus reads in IGV.

Should I just align the human RNA-seq to virus genome ,get the bam using STAR and load the bam file and the virus genome in IGV?

or I should create a human + virus genome ,and then get the bam file (STAR )?

Since I know which virus was found in this sample,can I just align the sample to the respective virus strain genome?

Any thoughts?

Thanks, Ron

[microfuge]

SRA has added a cool new tool (Under analysis alpha tab). For example https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR043396 (Herpes virus in human sample). They do a taxonomic assignment of reads. The software can be downloaded but most analysis is predone for many SRA entries.

Answer 1

[swbarnes2]

Quick and dirty approach is to align just to virus, but you might get human reads that would better align to human genome falsely aligning to your viral genome, because that' all you gave it to match to. Better is to align to viral and human genome together. The alignment will be more accurate like that.