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  • EMS causal mutation identification by NGS

    Dear all,

    I was recently struck by this paper http://www.ncbi.nlm.nih.gov/pubmed/21398646 where the authors used 75bp Illumina NGS to identify EMS-induced mutations in Arabidopsis. The procedure involves crossing two ecotypes and sequencing (1) the parental ecotype A, (2) the parental ecotype B and (3) the F2 generation with phenotype suppression.
    My question is: if one had to repeat this study, what would be the absolute minimum coverage for obtaining a chance for a reliable SNP detection? Assuming re-sequencing of the parental lines too. In the paper they suggest 6x-9x, so if I understand correctly one run with modern Illumina machines will be sufficient for the entire experiment, assuming perhaps nuclei extraction.

    Thanks a lot
    Last edited by giorgifm; 01-09-2012, 12:45 AM.

  • #2
    http://www.genetics.org/content/earl...1.136069.short might be of interest.

    Cheers,
    Ian

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