Project work

The goal of this week’s homework is to complete the alignment and read count generation of all the samples of your project data. You all had a first go at it during the HW of week 6. Now is the time to get back to that, change what needs to be changed and write a script that will perform the alignment for all your samples. The final step for this week should generate a table of read counts which you should read into R.

  1. Set up a github repository where you will store all your scripts, and ideally, even your report at one point. Send us the link to the repo. If you want to set it to private, you will have to grant us access, i.e. Friederike (friedue), Luce (lskrbnek), Merv (mfansler).
  2. Align all your samples. Ideally use a for-loop and/or a script, i.e. automate and standardize the task to a certain extent, but do remember that legibility is valuable, too.
  3. Generate a read count table.
  4. Read the read count table into R and perform the quality controls and processing steps that we discussed in class.

We also strongly encourage you to start reading up on the biological background of your samples so that you can put the results of the QC and explorations into their context. Always try to answer the question “Does this make sense?!” when generating a new plot.

If you need support, get in touch with Merv on Thursday, 3-4pm. Zoom details to follow.