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!
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!
Comment