Application of empty blast result

Question

[marongiu.luigi]

Just to be sure: what is the practical meaning of a blast empty hit?

I have done an alignment against microbial species and I am now running blast (both n and x) to remove false positives. In particular with blastx, I am getting a list of possible hits such as Eurkaryota, Viruses and Bacteria. But some hits are simply empty.

The meaning of an empty blast result is obviously that there was no hit on the database. But shall I keep the read or discard it? If, for instance, the point is to keep only viral hits, can I keep the empty reads on the ground that are not recognized as bacterial or human and probably define novel sequences (a bit far fetched)? Or shall I discard them because they are not confirmed (as viral)?

Thank you

[GenoMax]

Theoretically speaking you can keep the read since there is a chance that it could be a previously unknown organism (virus or something else). Practically it would depend on what you are doing with that data afterwards. Having unknown reads floating around is going to be just noise in your data.