Link to this document's Jupyter Notebook

In order to successfully complete this assignment you need to participate both individually and in groups during class. If you attend class in-person then have one of the instructors check your notebook and sign you out before leaving class on Monday January 25. If you are attending asynchronously, turn in your assignment using D2L no later than _11:59pm on Monday January 25.

In-Class Assignment: Getexample

Bowtie Software Logo

Agenda for today's class (70 minutes)

  1. (20 minutes) Preclass Review
  2. (10 minutes) Project Proposals (due Feb 11)
  3. (20 minutes) Bowtie Example
  4. (20 minutes) Getexample Discussion

1. Preclass Review

0121--Getexample_pre-class-assignment

Commands:

module list
module load powertools
powertools
getexample

As a class we will discuss the getexamples we tried, answer questions and see if we can get them working.

2. Project Proposals (due Feb 11)

We will take about 10 minutes in class to discuss project proposals which are due February 11th.

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.

✅ 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

As a class, we will 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 question here.

Congratulations, we're done!

If you attend class in-person then have one of the instructors check your notebook and sign you out before leaving class. If you are attending asynchronously, turn in your assignment using D2L.

Course Resources:

Written by Dr. Dirk Colbry, Michigan State University Creative Commons License
This work is licensed under a Creative Commons Attribution-NonCommercial 4.0 International License.