blastx parameters to return top 5 hits for each contigs

[super0925]

Hi
I performed a blastx of some thousand contigs and I want only top 5 hits for each contigs if it has more than 5 hits.
The result will go to Blast2GO to do GO mapping.

With this post I know http://seqanswers.com/forums/showthread.php?t=41875 blastall could do it.

Which is blastx -p blastx -b 1 - v 1(but it is only 1 hit)
Options from blastall
-v Number of one line descriptions
-b Number of alignments to show

(1) how about 5? is it -b 5 -v 5?
And e-value? I don't know which is better cause I saw some post said 1e-3 but some said 1e-6 is better.

(2) if I directly use blastx not the old version blastall, which parameter could I set?

-max_target_seqs
-num_alignments
-max_hsps

Thank you!

[GenoMax]

Is there a reason you are using an old version of blast (based on your references to blastall)?

If you want to keep using the old version for some reason then "blastall -help or blastx -help" should produce enough on-screen help that will help answer the question you have. You are basically on the right track.

It may help to understand e-value (http://journals.plos.org/plosbiology...l.pbio.1001014) before you decide if -3 or -06 is better for your intended purpose.

[super0925]

Is there a reason you are using an old version of blast (based on your references to blastall)?

If you want to keep using the old version for some reason then "blastall -help or blastx -help" should produce enough on-screen help that will help answer the question you have. You are basically on the right track.

It may help to understand e-value (http://journals.plos.org/plosbiology...l.pbio.1001014) before you decide if -3 or -06 is better for your intended purpose.

Hi GenoMax
Thank you for your help.
Let's go to latest version blastx help file
I am confused about the
-max_target_seqs <Integer, >=1>
Maximum number of aligned sequences to keep
* Incompatible with: num_descriptions, num_alignments

-num_alignments <Integer, >=0>
Number of database sequences to show one-line descriptions for
Not applicable for outfmt > 4
Default = `500'
* Incompatible with: max_target_seqs

-num_alignments <Integer, >=0>
Number of database sequences to show alignments for
Default = `250'


Which parameter shall I set for only get 5 hits for each contigs? -num_alignments or -num_alignments or -max_target_seqs

[super0925]

Is there a reason you are using an old version of blast (based on your references to blastall)?

If you want to keep using the old version for some reason then "blastall -help or blastx -help" should produce enough on-screen help that will help answer the question you have. You are basically on the right track.

It may help to understand e-value (http://journals.plos.org/plosbiology...l.pbio.1001014) before you decide if -3 or -06 is better for your intended purpose.

I got it.
It is -max_target_seqs 5
Thank you

[GenoMax]

Depends on what output format you are using. If you purely want to keep 5 hits then you would want to use num_alignments 5 and num_descriptions.

parameter -max_target_seqs is ignored for output formats, 0,1,2,3. Use -num_descriptions and -num_alignments to control output

[super0925]

Depends on what output format you are using. If you purely want to keep 5 hits then you would want to use num_alignments 5 and num_descriptions.

I want to ouput XML (option 5),
so either"-max_target_seqs" or " -num_descriptions and -num_alignments" works???

[GenoMax]

Either option works for XML output (-outfmt 5).