Blastn's "qcovus" is behaving odd, it seems to be giving artificially low scores
0
0
Entering edit mode
2.2 years ago
iddo.nadav ▴ 30

Hey all,

I'm using "qcovus" in my blast command in order to to retrieve only unique hits between two sequences (no overlap):

blastn -query q.fa -subject s.fa -outfmt "6 std qlen slen qcovs qcovus"

I'm getting a strange behavior..

q.fa and s.fa are single node genomes, with very similar length (<1% difference).

When I blast in one direction (a->b), I get: qcovs=96% and qcovus=96% When I blast the other way around (b->a), I get: qcovs=96% and qcovus=60%

This surprises me, I looked for some bug in the beginning, but everything seems to be working correctly. I dare not suggest Blast has a bug either. Can anyone explain what might be happening here?

Thanks

blast alignment • 502 views
ADD COMMENT
1
Entering edit mode

Blast will mask query sequences by default. Can you explicitly turn that off (-dust off) and see what you get?

ADD REPLY

Login before adding your answer.

Traffic: 1571 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

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

Powered by the version 2.3.6