Exercise 02

Aligning All Samples Exercise

15 Minutes

We just learned about how to use RSEM & STAR, but now we need to align all of the rest of our samples to the reference genome. In this breakout exercise, we’ll build upon some concepts we’ve learned previously.

Instructions:

• Work independently in the main room, posting any questions that arise to slack.
• Recommendations for writing your own code:
  • Read function documentation
  • Test out ideas - it’s okay to make mistakes and generate errors
  • Use a search engine to look up errors or recommended solutions using keywords
• We’ll review possible solutions after time is up as a group.

• Review what we’ve learned about running RSEM + STAR, to determine an appropriate command for aligning our samples.
• Using what we’ve learned previously, create a script using this command to quickly and easily align the rest of our samples.
• Run the script, view the output, and verify that we have the files we need.