Question: How to obtain only one target sequence for each query read using blast+?
gravatar for vitor.eca
10 weeks ago by
vitor.eca0 wrote:

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).

assembly • 179 views
ADD COMMENTlink modified 10 weeks ago by h.mon22k • written 10 weeks ago by vitor.eca0

ha, tricky question nowadays ;) (google for other posts here on biostar with the max_target_seq as keyword)

Long story short: you're better of running the blast with default values and then filter out only a single hit for each query in post-processing. Have a look here, 'trick 6' : (haven't tested that one myself though)

You mention 'read', is that read as in NGS or something different? If the former: blast is probably not the best approach then (unless you only have a very limited amount of reads to process)

ADD REPLYlink modified 10 weeks ago • written 10 weeks ago by lieven.sterck3.5k

Thanks lieven.sterck :)

ADD REPLYlink written 10 weeks ago by vitor.eca0
gravatar for h.mon
10 weeks ago by
h.mon22k wrote:

Don't -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.

ADD COMMENTlink written 10 weeks ago by h.mon22k
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