Hi,
I have downloaded the current version of the stand-alone-blast (ncbi-blast-2.2.29+) and I am trying to use blast (blastn) to find similarity of of a group of nucleotide sequences that I have. However, I am interested on only the top 3 matches. I tried searching online and I saw some posts that suggests using -K, but I realized this does not work with the new version that I am using. I looked at the help document and I tried using ( -max_target_seqs) and ( -num_alignments) but none of them worked. The result contains all the matches found by blast.
Does anyone know how to limit the results to let say just top 3 matches?
Thanks!