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  • How to output 5 top hits using standalone blast

    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

  • #2
    Adding "-num_alignments 5" will work.
    Last edited by GenoMax; 09-08-2017, 09:21 AM.

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    • #3
      GenoMax, I tried to use -num_alignments 5 and did not work...I got many hits.

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      • #4
        Originally posted by clarissaboschi View Post
        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?

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        • #5
          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.

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