Application of empty blast result
Entering edit mode
16 months ago

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

blast filtering empty • 237 views
Entering edit mode

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.


Login before adding your answer.

Traffic: 1261 users visited in the last hour
Help About
Access RSS

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6