How to be sure that the microbiome I obtained is sound?
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8 months ago

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

alignment sequencing next-gen assembly error • 196 views
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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

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