ICA 4: Getexample

ICA 4: Getexample#

Bowtie Software Logo

Agenda for today’s class (70 minutes)#

  1. (20 minutes) Preclass Review

  2. (10 minutes) Project Proposals (due Feb 5)

  3. (20 minutes) Bowtie Example

  4. (20 minutes) Getexample Discussion

1. Preclass Review#

Discuss with your group what you learned in the pre-class.

Commands:

module list
module load powertools
powertools
getexample

If you encountered issues, discuss them with your group and see if you can get them working. If you can’t get it working with your group, have an instructor help you get it working.

2. Project Proposals (due Feb 9)#

We will take a few minutes in class to discuss project proposals which are due February 9th. Take a look at the project description on the course website and start thinking about ideas.

3. Bowtie Example#

Bowtie is an ultrafast, memory-efficient short read aligner. It aligns short DNA sequences (reads) to the human genome at a rate of over 25 million 35-bp reads per hour. Bowtie indexes the genome with an FM index to keep its memory footprint small: typically about 2.2 GB for the human genome (2.9 GB for paired-end).

✅ DO THIS: Log onto the HPCC download the bowtie example using the getexample command and figure out how to run the example. See if you can answer the following questions. (The HPCC OS has been updated since this example was created so it may not work as is. If it doesn’t work, try removing the module load statements in run.sh and replacing them with “module load module load Bowtie2/2.5.1-GCC-12.3.0”)

✅ **QUESTION:**Does Bowtie have a shared memory or shared network paralization option?

Put your answer to the above question here.

✅ QUESTION: Which version of bowtie being used in the example?

Put your answer to the above question here.

✅ QUESTION: What directory is bowtie installed?

Put your answer to the above question here.

✅ QUESTION: Can you cat the bowtie executable?

Put your answer to the above question here.

✅ QUESTION: Can you ldd the bowtie executable?

Put your answer to the above question here.

✅ QUESTION: What language is the bowtie executable written in?

Put your answer to the above question here.

4. Getexample Discussion#

✅ QUESTION: Discuss what makes an example useful. What are good things to include and what are bad things to include?

✅ QUESTION: How does this discussion relate to the first part of your class project?

Put your answer to the above questions here.

Congratulations, we’re done!#

Have one of the instructors check your notebook and sign you out before leaving class.

Written by Dr. Dirk Colbry, Michigan State University (Updated by Dr. Nathan Haut in Spring 2025) Creative Commons License
This work is licensed under a Creative Commons Attribution-NonCommercial 4.0 International License.