Today I finished validating a CpG O/E workflow Steven put together by analyzing the C. gigas transcriptome and comparing it to the results of Gavery and Roberts (2010). The results agreed well. Notably, there was a similar bimodal distribution of CpG O/E, and major gene categories showed similar levels of CpG O/E (e.g., cell adhesion around 0.7 and DNA metabolism around 0.5).
Since mid-Oct 2014 I have been getting familiar with blasting transcriptomes using IPython. Steven helped me get set up with the first blast of Madracis and I’ve taken it from there. IPython notebooks can be found below.