Usage Guide

Welcome to the Dashing Turtle Quick Start Tutorial! This guide will help you get started with setting up sequences, loading data, running predictions, and generating landscapes.

Overview: Visual Workflow

[Add Sequences]
      │
      ▼
[List Sequences & Get LIDs (Visible in Graphical Interface)]
      │
      ▼
[Load Basecall Data]
[Load Signal Data]
      │
      ▼
[Run Predictions]
      │
      ▼
[Create Landscape]

Step 1: Add Your Sequences

Before running predictions, add at least two sequences:

  • One unmodified (control)

  • One modified

Example command:

seq -add -s GGAUCGAUCG -sec .......... -e EXP001 -n Testgoose -t 37 -t1 TypeA -t2 TypeB -r 1

Options:

  • -s: RNA sequence (A, C, G, U)

  • -sec: Secondary structure in dot-bracket notation (must match sequence length)

  • -e: Experiment name (required with -sec)

  • -n: Sequence name

  • -t: Temperature in °C (default: 37)

  • -t1, -t2: Type labels (e.g. modified vs unmodified)

  • -r: Run ID (default: 1)

Step 2: List Sequences & Get LIDs

Once added, list your sequences to obtain Library IDs (LIDs):

seq -list

Example output:

52 Unmodified Example Sequence
53 Modified Example Sequence

You’ll use these LIDs in subsequent steps.

Step 3: Load Basecall and Signal Data

Load basecall data:

load -basecall -l 52 -p Sample/DMSO/Alignment

  • -l: LID of the sequence

  • -p: Path to basecall alignment directory

Load signal data:

load -signal -l 52 -p Sample/DMSO/DMSO_fmn.txt

  • -l: LID of the sequence

  • -p: Path to signal file

Repeat for both modified and unmodified sequences.

Step 4: Run Predictions

Once data is loaded, run predictions:

predict -u 52 -l 53 -v

  • -u: LID of unmodified sequence

  • -l: LID of modified sequence

  • -v: (Optional) Include ViennaRNA base-pairing probabilities

Step 5: Create Landscape

Generate a landscape visualization using:

create_landscape -u 52 -l 53 -o

  • -u: LID of unmodified sequence

  • -l: LID of modified sequence

  • -o: Optimize clusters and output dendrograms

Cheat Sheet

Summary

  1. Add sequences (at least one unmodified and one modified)

  2. List sequences to find LIDs

  3. Load basecall and signal data

  4. Run predictions

  5. Generate a landscape visualization

You’re now ready to begin your Dashing Turtle data analysis workflow!