The computer cluster guys were great. They took extra pains to make sure we understood the big issues, they were really helpful in suggesting ways to optimize our runs, and they even gave us a tour of the WestGrid system.
I've cataloged the reverse-complement runs (same basic results as the forward runs), and made this composite logo based on all the USSs in the genome (i.e. both strands). It doesn't look any different than a composite logo I posted about 6 weeks ago; the difference here is that now I know I've done the right analysis.
Now on to analyzing the leading-strand and lagging-strand searches. I already did a quick-and-dirty version of that too, but again now I'll have done it well.
10 minutes ago in Variety of Life