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

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  • Adam Spargo
    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
    Message 1 of 3 , 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
      >
      >
      >
      >


      --
      The Wellcome Trust Sanger Institute is operated by Genome Research
      Limited, a charity registered in England with number 1021457 and a
      company registered in England with number 2742969, whose registered
      office is 215 Euston Road, London, NW1 2BE.
    • edburke1979
      Hi Adam, Thanks for the quick response. Do you have any idea of the amount of memory neccessary to build the hashtable of the Human genomic sequence? I am
      Message 2 of 3 , Oct 17, 2007
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        Hi Adam,

        Thanks for the quick response.

        Do you have any idea of the amount of memory neccessary to build the
        hashtable of the Human genomic sequence? I am running out of memory
        when trying to use skip of 1 and kmer of 12. We only have 1GB free on
        the server at the moment.

        Best Regards,

        Ed

        --- In ssahausers@yahoogroups.com, Adam Spargo <aws@...> wrote:
        >
        > 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
        > >
        > >
        > >
        > >
        >
        >
        > --
        > The Wellcome Trust Sanger Institute is operated by Genome Research
        > Limited, a charity registered in England with number 1021457 and a
        > company registered in England with number 2742969, whose registered
        > office is 215 Euston Road, London, NW1 2BE.
        >
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