[rhinoceros]

edit.
nevermind

[super0925]

Hi nr23,

Is this command could give you top 1 hit?
How about top 2 hits?
-max_target_seqs 1 -num_alignments 1 -num_descriptions 1

Thanks guys - I think I've got it down now:

this suggestion works well:

blastn -query your.fa -db your_db.fa -outfmt 6 | sort -k1,1 -k12,12nr -k11,11n | sort -u -k1,1 --merge > best_single_hits.blastn

But if you just want the names of query and top hit then:

blastn -db trop -query blast.fa -outfmt 6 -max_target_seqs 1 -num_alignments 1 -num_descriptions 1 -out results.out

cut -f 1,2 results.out > new.txt

more new.txt | uniq -u > singlehit.txt

N

[Aghatusha]

Same problem here

This multiple hits are appeared to be <Blast 2.2.29 versions bug with parameter -max_hsps_per_subject for tabular format (6).

Everything is working fine with -max_hsps 1 parameter in newer versions.