Question is in the title.
Is there a difference if I use default
-max_target_seqs settings in
blastn (which is 5, but can return 100s of hits due to many HSPs), then filter out the best HSP based on score from my outfmt file (I use
outfmt 6)? Versus just setting the
-max_hsps to 1 which essentially does the same thing?
I only need top hit and found that (at least for my samples), using default max target seqs just returned 100s of duplicates and never any different species matching to my query. Perhaps this is a case by case scenario?