Today's goal: Gibbs analyses

I've been trying to sort out the massive jumble of files that might be relevant to the US-variation manuscript, but I've pretty much decided that it's a waste of time. Instead I'm just going to focus on finding the files and sheets of paper where we have summarized what's been done and what we learned. And then I'll try to either find or create the specific files I need (depending on whether finding or re-creating looks easier).

For today, I'm not going to try to do anything about the Perl simulation work. Instead I'll just focus on the Gibbs analyses. I did find my instructions-to-myself of how to do these. I haven't heard back from the RS3 expert (apparently because his spam filter didn't like the urls in my email signature), so the first step now is to find what I've done to analyze these repeats. In particular, I have a N. meningitidis genome sequence from which the RS3 repeats have been removed; maybe I can figure out how I did this, and then test whether it makes a difference to the Gibbs results. And I also need to figure out why I seem to have been using two slightly different counts of the number of perfect 10-mer DUSs in the N. meningitidis genome.