BLAST+ Blastn - Discard hits below a certain score (length)

[kayleighepps]

Hi

I've been using the blastn (version 2.2.28+) standalone tool against a custom formatted genome via:

blastn -db BLASTDB -word_size 7 -query input.fa -out filename

Is there a command I can add to this to output only hits which are exact-matches (i.e. non-gapped) and which are above a certain length/score?

Thanks!

- Kayleigh

[kayleighepps]

Nevermind! This serves my purpose by giving me the top 2 perfect matches:

blastn -db BLASTDB -word_size 7 -query input.fa -out filename -perc_identity 100 -outfmt 7 -max_target_seqs 2