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Module 9 — The "View → Run → View" Loop (on a Real File)

Time: 60–75 min
Goal: Practice the core habit on your downloaded FASTQ.

Look before you loop

For a new dataset, always skim raw inputs and tool outputs before writing scripts.

The View → Run → View Workflow

graph TD
    A[New Dataset] --> B[View: head/tail/zless]
    B --> C[Understand Structure]
    C --> D[Run: FastQC/MultiQC]
    D --> E[View: Reports & Logs]
    E --> F{Quality OK?}
    F -->|Yes| G[Proceed to Analysis]
    F -->|No| H[Adjust Parameters]
    H --> D
    G --> I[Document Findings]

    style A fill:#e3f2fd
    style B fill:#fff3e0
    style D fill:#f3e5f5
    style E fill:#fff3e0
    style I fill:#e8f5e8

1) Inspect the data

cd ~/de-onramp/lesson5/data
zcat SRR.fastq.gz | head -n 8
zcat SRR.fastq.gz | awk 'NR%4==2{r++; bp+=length($0)} END{print "Reads:",r,"Bases:",bp}'

If you made SRR.10k.fastq.gz, use that for speed:

zcat SRR.10k.fastq.gz | head -n 8

cd ~/de-onramp/lesson5/data
gzcat SRR.fastq.gz | head -n 8
gzcat SRR.fastq.gz | awk 'NR%4==2{r++; bp+=length($0)} END{print "Reads:",r,"Bases:",bp}'

If you made SRR.10k.fastq.gz, use that for speed:

gzcat SRR.10k.fastq.gz | head -n 8

2) Run FastQC + MultiQC

mkdir -p ../qc && cd ../qc
fastqc ../data/SRR*.fastq.gz
multiqc .

Open multiqc_report.html. Note:

  • Per-base quality profile
  • GC distribution
  • Overrepresented sequences / adapter content
  • Sequence length distribution

3) Jot a mini-QC

Create ../qc/notes.txt with 4–5 bullets answering:

  • Is quality high and uniform across cycles?
  • Any adapters/overrepresented sequences?
  • Paired vs single-end expectations met?
  • What would you do next (trim? filter? align?)

Exit Ticket (email)

Subject: DE M9 Exit Ticket –
Paste:

  • 5 bullets from your notes.txt
  • One MultiQC screenshot (per-base quality or GC)