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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

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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.

158 total view(s), 32 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:

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Tags

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

NIBLSE Incubator: Intro to Command Line Coding Genomics Analysis

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

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