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Intro to Command Line Coding Genomics Analysis

By Rachael St. Jacques1, Max Maza1, Ray A Enke1

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

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

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.

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NIBLSE Incubator: Intro to Command Line Coding Genomics Analysis

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