This class has been running since 2010-11, on the following principle:
- autumn semester: isolate bacterial DNA, sequence using Illumina, assemble;
- spring semester: close assembly gaps, annotate genome.
As anyone following genomics knows, the times they are a’changing again and again, so this is less and less state-of-the-art. So we have decided to try a new course plan this year, taking advantage of the progress in bacterial genome sequencing with long PacBio reads.
Our new principle is, hopefully:
- autumn semester: isolate bacterial DNA, sequence using PacBio, assembly trivial, annotate genome;
- spring semester: RNA-seq under 2 growth conditions, experiments, Illumina sequencing and bioinformatics analysis.
“Hopefully” because PacBio on bacteria is not yet routine, depending on the genus and the growth conditions. We are thus trying two different bacteria, a Pseudomonas which has a cool story for the RNA-seq part, and a Caulobacter which has been shown to work with PacBio. Preliminary studies on the Pseudomonas are somewhat discouraging for the PacBio sequencing, but we will still try, with adaptations of the protocol. We will also keep the possibility to reverting to Illumina sequencing plus assembly, but we would like to avoid that (if Caulobacter is plan B, this is plan C).
And of course, we have never done RNA-seq with master students, so this year will be a new adventure, comparable to our first course in 2010. Stressful and exciting. 🙂