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Assignment 2

DSCI512: RNA-seq
Due date: November 13, 2016, 10:00am
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Make a supplemental figure from FASTQC output

Often when we use computational tools, we need to generate our own figure, say for supplemental material. One could copy and paste the images FASTQC spits out by default, but that is a little generic. Often, we tailor our own figures to each publication. This allows us to select the best font size, add annotations, and improve any descriptive text. Let's try it.

  • Navigate to the folder where your fastqc output was generated (from any sample).
  • Unzip the file <NAME> using $ unzip <NAME> where <NAME> is substituted with the real name of the sequence. This will create a directory containing the raw output of every plot. Raw data is stored in fastqc_data.txt.
  • Pick one plot type to work on. Either download or copy-and-paste the numbers necessary to generate that plot. Make your own plot. You can use excel, matlab, sigmaplot, R, whatever you like. This is a good time to talk to your PI about their preferred tools.
  • Make your own plot.
  • Make sure your axes are labeled.
  • Write a figure legend.
  • Bonus… make up some context or add some annotation of your own like an arrow or an extra label.
  • Save the figure and legend together in a .pdf
  • Upload the .pdf to canvas.

Files generated from FASTQC:

assignments/rna2018_assignment2.txt · Last modified: 2018/11/15 06:09 by erin