Explain two ways to run analysis - automated scripts vs individual modules

Added detailed explanation for beginners:

start_here.md:
- New section: '🎯 Two Ways to Run the Analysis'
- Option 1: Automated scripts (./tutorial.sh, ./run-analysis.sh) - RECOMMENDED
- Option 2: Individual module commands - for learning
- Explained what docker commands mean line-by-line:
  * docker run = run container
  * -v = share folders
  * python3 modules/... = run specific script
  * data/student_sequences/ = input
  * results/my_analysis/ = output
- Pros/cons of each approach

assignment.md:
- Added '💡 How to Run the Analysis' section at top of Part 1
- Clarified: Can use ./run-analysis.sh OR run steps individually
- Emphasized automated script is easiest
- Explained individual commands are for understanding/re-running steps
- Reminded: commands run in VSCode terminal, Docker is automatic

Benefits:
- First-time students understand they have options
- Know what's happening 'under the hood'
- Can troubleshoot by re-running individual steps
- Less intimidating - scripts do the work!

Author: cosmelab

assignment.md

@@ -48,6 +48,24 @@ The dataset includes:
 - Reverse reads (sample names ending in R)
 - Example: AT-HV1F and AT-HV1R are a pair
 
+---
+
+### 💡 How to Run the Analysis
+
+**OPTION 1 (RECOMMENDED): Use the automated script**
+```bash
+./run-analysis.sh
+```
+This runs all 6 steps below automatically. **This is the easiest way!**
+
+**OPTION 2: Run each step individually (shown below)**
+
+The commands below show you what happens in each step. You can run them one by one if you want to understand the process better, or if you need to re-run just one step.
+
+**These commands run in your VSCode terminal on your computer** - Docker is called automatically.
+
+---
+
 ### Step 1: Quality Control (10 points)
 
 Check which sequences are good enough to use:

start_here.md

@@ -104,6 +104,62 @@ ls
 
 ---
 
+## 🎯 Two Ways to Run the Analysis
+
+You can run the analysis in two ways:
+
+### Option 1: Automated Scripts (RECOMMENDED for beginners)
+
+**Easy, one-command approach:**
+```bash
+./tutorial.sh        # Runs all 5 steps automatically
+./run-analysis.sh    # Runs all 5 steps on your data
+```
+
+**Pros:**
+- ✅ Simple - just one command
+- ✅ Everything runs automatically
+- ✅ Can't mess up the order
+
+**This is what most students should use!**
+
+### Option 2: Run Each Module Separately (For learning)
+
+**If you want to understand what's happening, you can run each step individually.**
+
+The scripts use commands like this:
+```bash
+docker run --rm --entrypoint="" -v $(pwd):/workspace -w /workspace \
+  cosmelab/dna-barcoding-analysis:latest \
+  python3 modules/01_quality_control/qc_chromatograms.py \
+  data/student_sequences/ \
+  results/my_analysis/qc/ \
+  --open
+```
+
+**What does this mean?**
+- `docker run` = Run the Docker container
+- `-v $(pwd):/workspace` = Share your current folder with Docker
+- `python3 modules/01_quality_control/qc_chromatograms.py` = Run the QC Python script
+- `data/student_sequences/` = Input: where your .ab1 files are
+- `results/my_analysis/qc/` = Output: where results go
+- `--open` = Automatically open the HTML report
+
+**All individual commands are in `assignment.md` if you want to run steps one by one.**
+
+**Pros:**
+- ✅ Understand each step
+- ✅ Can re-run just one step if needed
+- ✅ See exactly what's happening
+
+**Cons:**
+- ❌ More typing
+- ❌ Easy to miss a step or mess up the order
+
+**For this assignment, we recommend using the automated scripts (Option 1).** But if you're curious about how things work, check out `assignment.md` for the individual commands!
+
+---
+
 ### OPTIONAL: Interactive Terminal (Advanced)
 
 **Want a fancy terminal with colorful output?** The container includes a beautiful Zsh shell setup!