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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
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
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