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Assignment 2

Due date: December 8, 2016, 10:00am

Exercise 1

Design an RNA-seq experiment pertaining to your own research. It might be an experiment you are actually doing, one you are planning to do, or one that is totally made up. Write a short pretend e-mail proposing the RNA-seq experiment to your PI or to a collaborator who will help you. Be sure to include the following:

  • A salutation and some introduction on your motivation for contacting the person
  • The biological question
  • The different conditions you will test
  • Your hypothesis or a general description of what you could expect to find
  • A description or list of follow up experiments you plan to do afterwards
  • Your name at the bottom and a formal signature on your email stating your lab, university, and contact info, etc

Exercise 2

Find a paper in your field that has performed RNA-seq. Read their methods section to determine how they performed and analyzed their RNA-seq experiment.

  • Provide a link to the paper you read.
  • List the software they used for analysis or state where they wrote custom scripts or algorithms.
  • Critique whether you think it would be relatively easy or hard to reproduce the analysis performed in the paper. Do the authors list software versions, the genome version, or the annotation file (.gff) version? Do the authors reference software used or provide a link to the software? Do the authors make their custom software or scripts available?

Exercise 3

Select one plot you produced in DESeq2 to turn into a figure. Import your plot into powerpoint (ok) or Illustrator (better) or some other comparable illustration software you plan to use for publishing your own figures. Turn the pdf generated from R into a publication quality figure with a legend. This may require modifying things like the axis text size or font. You may need to change the axis text itself (you can cover over the old one if you're using powerpoint) or overlay more text for clairty. You may need to add units to the legends. Be sure to include a formal Figure legend with a Figure title and a description of the figure and briefly how it was generated. Save your figure and legend together on the same page and upload it to canvas as a standard paper (letter) sized .pdf file.

Here are some .pdf's you can use in case you have trouble with the ones you generated in class. You only need to pick one:

ma_plot.pdf

sample_distance_plot.pdf

changing_genes.pdf

wiki2016_assignment2.txt · Last modified: 2016/12/05 19:52 by erin