[mira_talk] Re: ssaha2 parameters to perform perfect match
- From: Laurent MANCHON <lmanchon@xxxxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Thu, 18 Mar 2010 12:24:14 +0100
yes you are right,
now it returns only the matches with only 100% identity,
but not only on all the sequence length.
I want only 100% identity and also with 100% alignement on all the query
sequence length.
Lionel Guy a écrit :
Hi Laurent,
I haven't used it myself, but have you tried with the option -identity
100 (or 1, not sure) ?
From the manual:
-identity seqid Report only mappings with a pairwise sequence identity of
at least seqid. Other mappings are skipped. seqid specified the pairwise
sequence identity as a percentage of the alignment length.
Lionel
On 18 Mar 2010, at 12:06 , Laurent MANCHON wrote:
--Hi
is anybody know the correct parameters to use with ssaha2 to perform
perfect match ?
for instance when i use this command:
ssaha2 -kmer 8 -skip 1 -seeds 1 -score 12 -cmatch 9 -ckmer 6 -output
ssaha2 chr3.fa patterns.txt | grep '^ALIGNMENT'
it returns perfect match but not only, there are also results with
gap and mismatch alignment
thank you --
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