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105Re: [ssahausers] SSAHA2 setup to search for primer binding sites

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  • Adam Spargo
    Oct 12, 2007
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      Hi,
      To hit short reads allowing mis-matches you will need to use -skip 1, kmer
      12 is usually fine.

      Cheers.

      --
      Dr Adam Spargo
      High Performance Assembly Group email: aws@...
      Wellcome Trust Sanger Institute Tel: +44 (0)1223 834244 x7728
      Hinxton, Cambridge CB10 1SA Fax: +44 (0)1223 494919

      On Thu, 11 Oct 2007, edburke1979 wrote:

      > Hi,
      >
      > I am trying to setup SSAHA2 to search for primer binding sites in the
      > human genome. The app we currently have that does this uses BLAST, but
      > I would like to speed up the search.
      >
      > The primers will be 15-30bp and I want to allow for up to 2 mismatches
      > between query and target.
      >
      > I am planning to read the hashtable in from disk rather store in memory.
      >
      > Can anyone suggest some appropriate values for -skip and -kmer for
      > ssaha2Build?
      >
      > Best Regards,
      >
      > Ed
      >
      >
      >
      >
      > Yahoo! Groups Links
      >
      >
      >
      >


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