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DanceMaPper Pipeline Specification

Pipeline Details

  • Name: DanceMaPper
  • Pipeline UUID: c87e3c1962a7440194af651341ad730d
  • Version: 1.0.0
  • View Pipeline:

Overview

DanceMaPper pipeline is designed for analyzing high-throughput RNA structure probing data (e.g., SHAPE-MaP). It automates read preprocessing, alignment, mutation counting, and reactivity calculation, producing per-nucleotide reactivity profiles suitable for RNA secondary structure modeling.

Key Use cases:

  • RNA Secondary Structure Analysis: Processing SHAPE-MaP data to generate reactivity profiles for secondary structure prediction.
  • RNA Tertiary Structure Detection: Using RingMapper to identify correlated mutation events (RINGs) that report on RNA tertiary interactions.
  • Comparative Structure Analysis: Analyzing both modified and untreated samples to determine background-corrected reactivity profiles.

Features

  • Comprehensive RNA Structure Analysis: Integrates both secondary and tertiary structure analysis through DanceMapper and RingMapper 1.3.
  • RING and PAIR-MaP Detection: Detects correlated mutation events to identify both secondary structure base pairs and tertiary contacts.
  • Flexible Input Handling: Supports analysis with or without untreated control samples.
  • Advanced Clustering: Implements Bayesian mixture modeling with configurable components and fitting parameters.
  • Quality Control: Includes minimum coverage filtering and chi-squared cutoffs for robust analysis.
  • Visualization Support: Generates cluster analysis plots and secondary structure predictions.
  • Containerized Execution: Uses Docker container (quay.io/viascientific/dancemapper:1.0.1) for reproducible results.

Input/Output Specification

Inputs

Required

profile

  • Description: Profile file containing SHAPE reactivity profile or similar structured data used as input for analysis.
  • Format: .txt or .prof
  • Example File Path: /path/to/input/sample.prof

modified_mut

  • Description: Parsed mutations file from the modified sample containing mutation data for structure probing analysis.
  • Format: .mut
  • Example File Path: /path/to/input/modified_sample.mut

name

  • Description: Sample name or identifier used for output labeling, automatically inferred from profile base name.
  • Format: String
  • Example: sample_001

Optional Inputs

untreated_mut

  • Description: Parsed mutations file from untreated (control) sample for background correction.
  • Format: .mut file or placeholder (NO_FILE_*)
  • Example File Path: /path/to/input/untreated_sample.mut

min_cov_ceck & min_coverage

  • Description: Minimum read coverage filter parameters. min_cov_ceck enables the filter, min_coverage sets the threshold.
  • Format: Boolean string and integer
  • Options: "true"/"false" for min_cov_ceck, integer for min_coverage

fit_check

  • Description: Enable fitting mode during analysis for Bayesian mixture modeling.
  • Format: Boolean string
  • Options: "true"/"false"

pair_check

  • Description: Enable PAIR-mapping mode for detecting correlated mutations between paired nucleotides.
  • Format: Boolean string
  • Options: "true"/"false"

ring_check

  • Description: Enable RING-mapping mode for detecting correlated mutations across distant nucleotides.
  • Format: Boolean string
  • Options: "true"/"false"

Outputs

Reported Outputs

  • DanceMapper Results Directory:
  • Description: Complete output directory containing reactivity profiles, BM files, and analysis results
  • Format: Directory containing multiple file types (.bm, .txt, .bp)
  • Example File Path: /output/dancemapper_results/

  • Location: Main output folder

  • Cluster Analysis Results:

  • Description: Secondary structure predictions and folding analysis for each cluster
  • Format: Directory containing structure files and predictions
  • Example File Path: /output/cluster_analysis/
  • Location: Analysis folder

Supporting Outputs

  • Cluster Visualization:
  • Description: Optional plots and visualizations of cluster analysis results
  • Format: Image files (PNG, PDF)
  • Example File Path: /output/cluster_plots.png
  • Visualization App: Standard image viewers

Associated Processes

References & Additional Documentation

  • Related Papers/links: Static Badge
  • Pipeline Repository: Zenodo Repository
  • Workflow Diagram: Available in pipeline description pages