I am currently analyzing RNAseq data based on 16 lung cancer tumor samples. While testing for fusions with different algorithms, I added the parameters to look for reads mapping to viral genomes in fusionCatcher, just because I could. It uses the following DB : ftp://ftp.ncbi.nlm.nih.gov/genomes/Viruses/ and I got in almost all my patients, reads mapping (ranging from 50 to 700) to a repeating 3-4 viral genome. I am looking for advices/insights into what is available to me if I want to make sense of all this and confirm/infirm that information. If anybody has gone through the process I would greatly appreciate your input.
Have a great day,