Can -num_alignments influence the outfmt 6 blast output format?

Question

[flogin]

Hello guys, I was reading about the basic parameters of BLAST+, I used to set the parameters -outfmt 6 to return a tabular file as output with 12 columns.

But I have one question about the parameter -num_aligments.

If, for example, I set -num_aligments 5, in my tabular output only 5 lines per query will be written? or this parameter only works for the output in formats =< 4?

Best.

Answer 1

[GenoMax]

Correct. You actually get n+1 alignments. If you select less than 5 blastn will give you a warning

Warning: [blastn] Examining 5 or more matches is recommended

This has to do with a bug that was fixed in blast+ package.

That said you may want to control the number by using -max_target_seqs instead.

[flogin]

Thanks genomax,

I was reading and making some tests, the -num_alignments will show N alignments per HSPS between query-subject right?

So can I combine -num_alignments 5 with -max_hsps 1, for example, to recovery only 5 lines per query?