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DanceMapper Specifications

Process Details

  • Name: DanceMapper
  • Process UUID: 42f27cd80b00436c888d2e7ed9609144
  • Process Group: Misc.

Overview

DanceMapper is a pipeline for RNA structure probing data (e.g., SHAPE-MaP), handling read preprocessing, alignment, mutation counting, and reactivity profiling. Version 1.1 includes RingMapper 1.3 to detect correlated mutation events ("RINGs"), enabling analysis of both secondary and tertiary RNA structure.

This process is implemented in Bash, which invokes Python scripts for RNA structure analysis using DanceMapper.

Key Functionality

  • RNA Structure Probing Analysis: Processes SHAPE-MaP data for comprehensive RNA structure characterization
  • PAIR-mapping: Detects correlated mutations between paired nucleotides to infer RNA secondary structure interactions
  • RING-mapping: Identifies correlated mutations across distant nucleotides to capture tertiary RNA contacts
  • Reactivity Profiling: Generates mutation counting and reactivity profiles from processed sequencing data

Input/Output Specification

Inputs

Required Inputs

  • Input File Text

    • Description: Configuration file containing sample and analysis parameters
    • Format: TXT

  • Modified Mutation File

    • Description: Mutation data from modified/treated RNA samples
    • Format: MUT

Optional Inputs

  • Untreated Mutation File
    • Description: Mutation data from untreated/control RNA samples for background correction
    • Format: MUT

Outputs

  • Analysis Directory
    • Description: Complete output directory containing all DanceMapper analysis results including reactivity profiles, structural predictions, and correlation analyses
    • Format: Directory

Parameters & Settings

These parameters can be adjusted in the Foundry UI when running this process.

  • Minimum coverage

    • Description: Minimum coverage. Please write the coverage after checking the box.
    • Default value: false

  • Minimum coverage - specify the coverage (integer)

    • Description: Minimum coverage (integer number of nts) required for a read to be included in calculations
    • Default value: (empty)

  • Fit data

    • Description: Flag specifying to fit data
    • Default value: true

  • PAIR analysis

    • Description: Checking this enables PAIR-mapping, detecting correlated mutations between paired nucleotides to infer RNA secondary structure interactions.
    • Default value: true

  • RING analysis

    • Description: Checking this enables RING-mapping, detecting correlated mutations across distant nucleotides to capture tertiary RNA contacts.
    • Default value: true

  • Minimum rxbg

    • Description: Set nts with rx-bg less than this to inactive
    • Default value: 0.002

  • Chi-squared cutoff

    • Description: Set chisq cutoff for RING/PAIR-MaP analysis
    • Default value: 23.9

  • Undersample

    • Description: Only cluster with this number of reads. By default this option is disabled (-1) and all reads are used
    • Default value: -1

  • Force fitting

    • Description: Force fit to specified number of components. Please write the number of components after checking the box.
    • Default value: false

  • Force fitting - specify the number of components

    • Description: (empty)
    • Default value: (empty)

  • maskG

    • Description: set all Us to inactive
    • Default value: false

  • maskU

    • Description: set all Gs to inactive
    • Default value: false

  • maskN

    • Description: set all Ns to inactive
    • Default value: false

  • Other Parameters

    • Description: Please see the other main parameters that can be entered here from DanceMaPper documentation. Options for fitting data: --maxcomponents MAXCOMPONENTS: Maximum number of components to fit (default=5); --trials TRIALS: Maximum number of fitting trials at each component number (default=50); --badcol_cutoff BADCOL_CUTOFF: Inactivate column after it causes a failure X number of times after a valid soln has already been found (default=5); --writeintermediates: Write each BM solution to file with specified prefix. Will be saved as prefix-intermediate-[component]-[trial].bm; --priorWeight PRIORWEIGHT: Weight of prior on Mu (default=0.01). Prior = priorWeightreadDepthbgRate at each nt. Prior is disabled by passing -1, upon which a naive prior is used. Options for performing RING/PAIR analysis on clustered reads: --window WINDOW: Window size for computing correlations (default=1); --readprob_cut READPROB_CUT: Posterior probability cutoff for assigning reads for inclusion in ring/pairmap analysis. Reads must have posterior prob greater than the cutoff (default=0.9). If set to -1, assign reads using maximum a posteriori (MAP) criteria; --mincount MINCOUNT: Set mincount cutoff for RING/PAIR-MaP analysis (default = 10); --pm_secondary_reactivity PM_SECONDARY_REACTIVITY: Set secondary_reactivity cutoff for pairmapper analysis (default = 0.4); --inclwindow: Include considered windows in read probability calculation and assignment. By default windows are EXCLUDED from calculations. Optional arguments: --readfromfile READFROMFILE: Read in solved BM model from BM file; --ignore_untreated: Ignore untreated mutation rates from profile.txt file. If ShapeMapper was run without an untreated sample, this argument is superfluous. Untreated rates are used for establishing priors during fitting, and computing normalized rates; --oldDMSnorm: Use old style (pre-eDMS) normalization; --suppressverbal: Suppress verbal output
    • Default value: (empty)

References & Resources

  • Tool Documentation: Contact the team for details on DanceMapper.py