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  • which program(s) to use?

    Hi,
    Can anyone recommend which program(s) to use to analyze my data?

    we are studying the mutation rate of mitochondrial DNA. Our data set consists of 3 samples from wild-type mice and 3 samples from a mutant strain of mice. We have performed ~20 million deep sequencing reads on mitochondrial DNA extracted from each sample. We would now like to ascertain the number of mutations present in each sample by comparing the reads to a reference copy of the mitochondrial genome. In the end we would like to do a quantitative comparison of the number of mutations present in the wild-type and mutant mouse samples. We don't necessarily need an assembly of the sequence reads or the identity of the mutations. For our first pass, we would just like to know how many mutations there are and maybe some general statistics about the nature of the mutations (SNP, del=
    etions, insertions, etc).

    Thanks a bunch!

  • #2
    whoa you posted at 3:33 am. creepy!

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