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Old 09-08-2017, 07:54 AM   #1
clarissaboschi
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Default 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
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Old 09-08-2017, 09:06 AM   #2
GenoMax
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Adding "-num_alignments 5" will work.

Last edited by GenoMax; 09-08-2017 at 09:21 AM.
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Old 09-08-2017, 01:10 PM   #3
clarissaboschi
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GenoMax, I tried to use -num_alignments 5 and did not work...I got many hits.
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Old 09-11-2017, 03:43 AM   #4
SylvainL
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Quote:
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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Old 09-11-2017, 04:02 AM   #5
GenoMax
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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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