Question: Can -num_alignments influence the outfmt 6 blast output format?
0
gravatar for flogin
12 months ago by
flogin250
Brazil
flogin250 wrote:

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.

blast parameters • 587 views
ADD COMMENTlink modified 12 months ago by genomax92k • written 12 months ago by flogin250
3
gravatar for genomax
12 months ago by
genomax92k
United States
genomax92k wrote:

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.

ADD COMMENTlink modified 12 months ago • written 12 months ago by genomax92k

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?

ADD REPLYlink written 12 months ago by flogin250
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1905 users visited in the last hour