Hello,
I have carried out a virome study from human samples. I have removed the sequences with below 33 phred-score, I ran BLASTN and BLASTX and removed everything that gave bacterial outcome to concentrate on viral sequences. The sequences I got do not result in the species reported as contaminants as such Afipia, Aquabacterium , Asticcacaulis, Aurantimonas, Acidovoraxc, Azoarcus, Azospira, Burkholderiad, Deinococcus etc etc or those reported by Eisenhofer (Trends in Microbiology, February 2019, Vol. 27, No. 2).
Can I rely upon the sequences that I have found? can I be sure -- relatively -- that the mapping is genuine or shall I fear the first reviewer of the work? I don't have DNA left for a confirmatory PCR; thus, I have to trust the mapping. But can it be trusted?
Thank you
Hi, What have you improved since you posted here? I'm working with virus metagenomics as well and I'm consolidating blast outputs from several virus specific DBs. May I ask what was the blast parameters and DBs you used? Cheers