1. Use featureCounts to count the number of reads that overlap with every exon. As usual, keep track of all the commands. Briefly explain at least 2 parameters (and their consequences!) that you’re using (can include parameters set to default mode, but not parameters that specify input and output file names). (3 points [plus up to 2 extra-credit points if you go beyond the standard display])
  2. Read the summary files generated by the featureCounts run we did during class and the one you just did into R. Generate a bar plot (using ggplot2) that displays the numbers of assigned and unassigned reads for either featureCounts run. The plot below is an example, you do not need to generate an exact replicate (you may also have run your featureCounts with slightly different parameters, so you may not even be able to replicate it exactly). (3 points)
  3. State at least two observations from the plot. (2 points)

Compile the .Rmd file and push both the .Rmd and the HTML files to your GitHub repo by Monday night.

(8pts)