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  • drio
    replied
    Post here a screenshot of the alignments (tablet) for one of the snps and then we can discuss. The original SAM alignments for the SNP would help also.

    Leave a comment:


  • biocc
    replied
    thanks

    Originally posted by drio View Post
    If you have a very small number of SNPs, validate them by eye. Display the alignments at the SNP position and see if the call makes sense. Ultimately of course validate via sanger.
    yes, i did it by eye through Tablet. i found some reads aligned are A and some aligned are G. if all these reads are unique, how should i determinate? thaks

    Leave a comment:


  • drio
    replied
    If you have a very small number of SNPs, validate them by eye. Display the alignments at the SNP position and see if the call makes sense. Ultimately of course validate via sanger.

    Leave a comment:


  • ntremblay
    replied
    Hi,

    if you encounter an interesting SNP in your analysis, the quickest way to determine if it's real or not would be to confirm it with an independant method like PCR + Sanger ...

    Leave a comment:


  • svl
    replied
    It could be a heterozygous SNP. Also errors can/will always occur (in sequencing, mapping), you might want to look at quality values as well.

    Leave a comment:


  • biocc
    started a topic how to determine a snp ?

    how to determine a snp ?

    hi, i resequenced a mutated bacteria genome, and want to detect the mutation information. at a position, i found half of the reads mapped are different from the reference, and half are the same . so some software reported it as snp, and some not. how to determine it as a SNP. how did this happened.
    thanks.

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