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  • 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!

  • #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
    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?

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    • #3
      hello everyone
      I am a new member

      Comment

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