Exercises

  1. Make a folder in which you’re going to keep track of everything related to your homework for the ANGSD class. (UNIX)
  2. Download the files containing the lengths of the individual yeast (S. cerevisiae) chromosomes for every genome assembly that is available at the UCSC Browser (hint: these should be very small text files ending with “chrom.sizes”; you can find them via the links to “Full data set” once you’ve tracked down the site for the yeast genomes). (UNIX)
  3. Compare the files of the different assemblies. What do you notice? (UNIX, common sense)
  4. Make a table listing the sizes for every chromosome across the 3 different assemblies. (Rmarkdown)

Make sure to document every step of your analysis that is relevant to the final results you’re presenting. It’s fine to also note if you manually copied and pasted entries, but we (and your future self) want to know exactly how you obtained every piece of information and how any visualizations or summaries were achieved.

Compile the .Rmd file and send both the .Rmd and the HTML files to angsd_2019@zoho.com by Sunday night.