Practicals for Sept/Oct 2020 Genome Bioinformatics module at qmul.
Prerequisites (we’ll cover this sepeartely)
We suppose that you are at ease:
- in the command line. For a refresher, try the SIB’s UNIX fundamentals online course.
- with R. The swirl() library/course can help:
- follow the R programming self-led course (skip the sections Simulation and Dates and Times)
- follow at least the ggplot section of the Exploratory_Data_Analysis swirl course
- Short read cleaning: Illumina short read cleaning
- Reads to genome: genome assembly, quality control
- Gene prediction: gene prediction, quality control
- Population sequencing to genotypes to population genetics statistics:
Computers should be set up as necessary to do all of this. It may alternatively be possible to do all of this on Apocrita or on QMUL’s Linux VDI (Virtual Desktop). It could also be feasible to do some of this stuff on a your favorite cluster or your local machine. However, it will be complicated. Among other things you’ll need to install a bunch of software and data.
The initial version of this practical was put together by * Yannick Wurm @yannick__ * Oksana Riba-Grognuz’ contributions for the 2012 edition of this course
It was heavily heavily heavily revised and improved thanks to efforts and new content by
Special thanks to Tom King, Tom Bradford, Simon Butcher, Sam Court, ITS and ITSResearch for setting up computers and clusters at QMUL so they just work.
Things used in other versions of this course:
Inferring population sizes and gene flow. (Credit Stefan Schiffels @stschiff) Gene expression ( Credit Julien Roux www @_julien_roux):