Module 4: Recap Exercises

Overview

This module brings together everything from Modules 1–3. There are no new concepts to learn — instead, you will apply what you already know to increasingly challenging problems, all using real data from the Training/ folder.

The exercises are designed for class discussion. There is often more than one correct answer. The goal is not just to get the right output, but to be able to explain why you chose your approach and what tradeoffs exist.

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How to Use This Module

• Work through each exercise set in order — they build on each other.
• Discuss your approach with the class before running any commands.
• When you disagree with a classmate’s approach, try both and compare the results.
• The Solutions file is there to check your work, not to shortcut the thinking.

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Exercise Sets

File	Difficulty	Topics
Exercise_1_Linux_Foundations.md	Easy → Medium	Navigation, file inspection, permissions
Exercise_2_Text_Processing.md	Medium	Pipes, grep, sort, counting reads
Exercise_3_Conda_and_Environments.md	Medium	Conda concepts, environments, channels
Exercise_4_Omics_Integration.md	Hard → Challenge	Full omics workflows, QC, assembly
Solutions.md	—	All solutions with explanations

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Training Data Reference

All exercises use files in the Training/ folder:

Training/
├── long_reads/
│   ├── barcode57.fastq       # Nanopore reads, 34,268 lines (8,567 reads)
│   ├── barcode58.fastq       # Nanopore reads, 36,784 lines (9,196 reads)
│   └── sample3.fastq         # Nanopore reads, 11,880 lines (2,970 reads)
└── short_reads/
    ├── paired/
    │   ├── SRR1553607_1.fastq  # Illumina forward reads, 203,445 reads
    │   └── SRR1553607_2.fastq  # Illumina reverse reads, 203,445 reads
    └── unpaired/
        ├── SRR11282407_Case.fastq.gz
        ├── SRR11282408_Healthy.fastq.gz
        ├── SRR11282409_Healthy.fastq.gz
        ├── SRR11282410_Case.fastq.gz
        ├── SRR11282411_Healthy.fastq.gz
        ├── SRR11282412_Case.fastq.gz
        ├── SRR11282413_Healthy.fastq.gz
        └── download.sh

Tip: Set a variable at the start of your session to save typing:

TRAINING=~/path/to/Training

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Difficulty Scale

• Easy — One command, covered directly in class
• Medium — Requires combining 2–3 concepts
• Hard — Requires thinking about the problem before writing any commands
• Challenge — Open-ended; there is no single correct answer