[mira_talk] Re: vector clipping

On Tuesday 10 March 2009 Jan Paces wrote:
> I have one project involving BACs sequencing on 454 Titanium. I tried to
> clip vector using ssaha:
>
> ssaha cra_in.454.fasta vector.fasta -d0 -p  >cra_ssahavectorscreen_in.txt
> [...]

Hi Jan,

found the problem. ssaha must be invoked like this:

ssaha vector.fa cra_in.454.fasta -da 0 -pf >cra_ssahavectorscreen_in.txt

That is, first the file with the vector sequences, then the file with the 
sequencing data. I'm not sure whether this is the "correct" order as ssaha 
defines it, but when I implemented the parsing options I made some tests during 
which I found out that ssaha somehow lost valid hits when it was called the 
other way round.

As a side question: are you perhaps using an older version of "sff_extract" to 
create the input files for mira? In the files you sent me, the XML looks like 
it 
... it has quality clips instead of sequencing vector clips.

Regards,
  Bastien 



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