settings for the best hits in commandline blast

[kaps]

Hi,

How can I set for the best 10 hits when blasting with command line blast?
kaps

[sarvidsson]

Did you try

-max_target_seqs 10

?

"Best" doesn't mean the same thing to everyone - but max_target_seqs should select the hits with the highest e-value and bit score.

[kaps]

yes,
but its like -max_target_seqs 10 does not give 10 maximum hits since i am getting many hits, more than 10!!

[sarvidsson]

Could you post the results? Often you get several (partial) alignments against one database sequence, which then counts as one "target sequence".

[kaps]

Attached is a txt file with the results.
I wait for your comments!

[sarvidsson]

As far as I can see, there are only one query with more than ten result lines (query 4_S4_L001_R1_001_(paired)_trimmed_(paired)_contig_23); in that case, one database target sequence has two alignments. This is the expected behaviour.

[ssully]

You are getting the 10 best target sequences for each query. For some of the queries, there is more than one hit (hsp) to the target. Those are returned too, so sometimes there are more than 10 lines per query. This is good behavior, e.g. if your query is cDNA and the target is a gene with an intron, the query is split into two matches.