Support

Support Options

  • Knowledge Base

    Find information on common questions and issues.

  • Support Messages

    Check on the status of your correspondences with members of the QUBES team.

Contact Us

About you
About the problem
Close
Close
You are here: Home / Resources / OER Products / Teaching Materials / A Fun Introductory Command Line Exercise: Next Generation Sequencing Quality Analysis with Emoji! / About

A Fun Introductory Command Line Exercise: Next Generation Sequencing Quality Analysis with Emoji!

By Rachael St. Jacques1, Max Maza1, Sabrina Robertson2, Guoqing Lu3, Andrew Lonsdale4, Ray A Enke5

1. Department of Biology, James Madison University 2. Department of Psychology & Neuroscience, University of North Carolina at Chapel Hill 3. Department of Biology and School of Interdisciplinary Informatics, University of Nebraska Omaha 4. ARC Centre of Excellence in Plant Cell Walls, Melbourne University 5. James Madison University

This resource is a fun computer-based intro to command line programming. The activity takes FASTQ NGS data files and runs a fun program called FASTQE.

Listed in Teaching Materials | resource by group NIBLSE Incubator: Intro to Command Line Coding Genomics Analysis

Download (DOCX)

Version 1.0 - published on 28 Feb 2019 doi:10.25334/Q4P733 - cite this Last public release: 2.0

Licensed under CC Attribution-ShareAlike 4.0 International according to these terms

View most current public release [2.0] for latest usage information.

193 total view(s), 51 download(s)

fastqe.png

Description

The activity takes FASTQ NGS data files and runs a fun program called FASTQE. This program is very similar to the popular FastQC, however, rather than outputting data plot visualizations of NGS sequence quality, FASTQE outputs emojis signifying the quality of each base call in the file. The activity takes a fundamental yet sort of boring step in NGS analysis and makes it accessible and fun to students without much experience in the field. It is also designed to for students with little to no experience using command line analysis to learn and run a few simple commands. The elated reaction from students when they get a long string of emojis to output after typing a few commands is really cool! The activity also utilizes another command line tool called FASTP for FASTQ file trimming and filtering.

Contents:

Cite this work

Researchers should cite this work as follows:

Tags

  1. 1 Hour
  2. Activity Length
  3. Advanced
  4. APC
  5. Audience Level
  6. bioinformatics
  7. BLAST
  8. C2. Computational concepts
  9. C4. Bioinformatics tools
  10. C5. Data retrieval
  11. C7. Scripting
  12. colon cancer
  13. command line
  14. data science
  15. emoji
  16. FASTP
  17. FASTQ
  18. FASTQE
  19. genetic testing
  20. genomics
  21. High School
  22. Illumina sequencing
  23. Incubated at NIBLSE
  24. Instructional Setting
  25. introductory
  26. Lab
  27. Lecture
  28. linux
  29. Mac
  30. Majors
  31. microbiome
  32. NCBI
  33. next generation sequencing
  34. NGS analysis
  35. NIBLSE
  36. Non-majors
  37. pedigree
  38. Phred score
  39. programming
  40. quality control
  41. short read
  42. Teaching material
  43. terminal
  44. Trimming
  45. Undergraduate

NIBLSE Incubator: Intro to Command Line Coding Genomics Analysis

NIBLSE Incubator: Intro to Command Line Coding Genomics Analysis group image

When watching a resource, you will be notified when a new version is released.

Adapt 0
Close

Home

Search