Day 1 - Breakout 02

Aligning All Samples Exercise (Breakout):

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. We’ll use the concepts we’ve learned earlier in this breakout exercise.

Instructions:

• One group member should share their screen in the breakout room. If nobody volunteers, a helper may randomly select someone.
• The group members should discuss the exercise and work together to find a solution.
• After a solution is found, allow time for all members to complete the exercise.

• Review what we learned about running RSEM + STAR, to construct an appropriate command for aligning one of our samples.
• Use a bash variable in our alignment command to quickly and easily align samples 2-4.
• View the output, and verify that we have the files we need.