Hi, I´m using blast+ (blastn) to do a local blast with a database I´ve downloaded. As a result I would like to have only one hit per each read I have, so, I´m using the option "max_target_seqs 1", it happens that sometimes I get more than one hit for each of my query sequences, for what I understand my query reads are matching with the same target sequence in different forms. Anyone knows an option that could give me only one hit? I´ve tried the option max_hsps 1 but this allows each target sequences to be hit only one time, which I don´t want, once several of my reads may probably correspond to the same target read (in my case, the same species).
-max_target_seqs 1 -max_hsps 1 together do what you want?
But you should be aware
-max_target_seqs 1 isn't a filter after all alignments have been found, rather, it changes the heuristics of the algorithm - see What BLAST's max-target-sequences doesn't do.