11.6.1. Amplicon sequence selection

  1. Illumina sequencing and BSMAP mapping results can be confirmed by 454 sequencing of a set of bisulfite amplicons.
  2.  Specific amplicon sequences are selected using raw methylome data and the following arbitrary criteria:
    1. Minimum coverage - 5 mapped reads for each queen and worker sample.
    2. Minimum 2 methylated CpGs within a region of ~400-600 bp of sequence showing at least 50% difference in methylation levels between the two samples.  This selection is very stringent, but assures that amplicons with high probability of differential methylation are selected.
  3. In addition a few regions of mtDNA that is not methylated are selected as controls (optional).