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  • genelab
    Member
    • Nov 2009
    • 27
    #1

    Find SNP in Sanger sequenced gene

    Hi guys,
    I have about 120 sequences of the same genes from our sample, which are sequenced by Sanger methods, How can I get the SNP sites among this gene compared to the reference gene? Is there any software can help me do this?

    Any sugestion will be highly appreciated!
    Tags: None
    • dagarfield
      Member
      • Aug 2010
      • 39
      #2
      My recommendation would be to align the reads to your reference using the long read option in BWA or Lastz (or something else with long read capacity) and output a SAM file. You should be able to get SNPs out of the SAM file pretty easily following the SAM Tools FAQ here
      SAM tools
      http://sourceforge.net/apps/mediawiki/samtools/index.php?title=SAM_FAQ
      Download SAM tools for free. SAM (Sequence Alignment/Map) is a flexible generic format for storing nucleotide sequence alignment. SAMtools provide efficient utilities on manipulating alignments in the SAM format.


      Will that do the trick?

        Comment

        • shayeste
          Junior Member
          • Mar 2014
          • 2
          #3
          hello everyone
          I am a new member

            Comment

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