How to output 5 top hits using standalone blast

[clarissaboschi]

I am using blast, and I would like to filter my results, not based on the best hit, but the top 5 hits.

I do not want to use the option "-max_target_seqs" because it does not result in the correct number, and also it was reported some issues with this option.

Any suggestions?
My output is: -outfmt '7 qseqid sseqid pident evalue bitscore stitle length'

thanks

[GenoMax]

Adding "-num_alignments 5" will work.

[clarissaboschi]

GenoMax, I tried to use -num_alignments 5 and did not work...I got many hits.

[SylvainL]

GenoMax, I tried to use -num_alignments 5 and did not work...I got many hits.

Are you sure all these hits do not have the same score?

[GenoMax]

You are probably getting more than one HSP per "accession hit". If you strictly want to limit that to one HSP per accession then you could try adding "-max_hsp 1". Keep in mind that adding these restrictions may cause you to miss some important hits.