User Tools

Site Tools


assignments:rna2018_assignment6

Assignment 6

DSCI512: RNAseq
Due date: December 11, 2016, 10:00am
Submit your assignment on canvas


Project description

Start a DESeq2 analysis project using the C.elegans dataset you generated in Assignment 5

  • Make a directory on your local computer called PROJ09_ce_deseq
  • Set up a sub-directory structure: 01_input, 02_scripts, 03_output

Import the data and script template

  • Import your counts.txt file from PROJ07_ce_homework2 (on summit) into the PROJ09_ce_deseq/01_input directory
  • Import your metadata file from PROJ07_ce_homework2 (on summit) into the PROJ09_ce_deseq/01_input directory
  • Copy the script from class today into the PROJ09_ce_deseq/02_scripts directory.

You can also download the input datasets here:

SCRIPT

Download the script 181206_Celegans_DESeq2.R at this site and place it in your directory called 02_scripts:

** Extra stuff… Try identifying an interesting gene in DESeq2 and look it up on the UCSC Genome browser I prepared and on Wormbase. Sadly, the UCSC Genome browser doesn't yet have standardized Wormbase ID's uploaded (in the form “WBGENE#####). You'll need to look up the “Sequence Name” on Wormbase first.


Turn in the following

Turn in a differential expression figure. Select a DESeq2 generated figure from EITHER the yeast or C. elegans dataset. Export if from RStudio by either using a pdf command or by clicking export from the Plots Window.

Modify your plot in Photoshop, Illustrator, or Powerpoint, or any other graphics software.

Add some annotation

Add a legend.

Upload your final figure as a .pdf to canvas.

Hints: Try using Arial font instead of exported font. Try making lines thinner or fatter. Maybe highlight a cool gene. Add some color. Add a legend.


Notebook

  • Make notes of what you did for this homework in your computational notebook.
  • Turn this in with your notebook at the end of the semester.
assignments/rna2018_assignment6.txt · Last modified: 2018/12/06 09:17 by erin