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ShapeMapper Specifications

Process Details

  • Name: ShapeMapper
  • Process UUID: f931vh4zwsfikgzckg0pvdhn38wa44
  • Process Group: Misc.

Overview

ShapeMapper automates the calculation of RNA chemical probing reactivities from mutational profiling (MaP) experiments. This process analyzes RNA structure by processing sequencing data from chemical probing experiments to generate reactivity profiles that reveal RNA secondary structure information.

This process is implemented in Bash, which invokes the ShapeMapper2 tool for RNA chemical probing analysis.

Key Functionality

  • Chemical Probing Analysis: Processes mutational profiling data from SHAPE-MaP and DMS-MaP experiments to calculate RNA reactivities
  • Multi-Sample Processing: Handles modified, untreated, and denatured samples in paired or unpaired configurations
  • Sequence Alignment: Supports both Bowtie2 and STAR aligners for optimal alignment of different RNA lengths
  • Quality Control: Applies comprehensive filtering based on mutation frequency, sequencing depth, and mapping quality
  • Visualization: Generates flowcharts and mutation profiles in multiple output formats

Input/Output Specification

Inputs

Required Inputs

  • Target RNA Sequence

    • Description: FASTA file containing the target RNA sequence(s) for analysis
    • Format: FASTA (.fa)

  • Modified Sample Directory

    • Description: Directory containing sequencing data from chemically modified RNA samples
    • Format: Directory containing FASTQ files

  • Untreated Sample Directory

    • Description: Directory containing sequencing data from untreated control RNA samples
    • Format: Directory containing FASTQ files

  • Mate Configuration

    • Description: Specifies whether samples are paired-end or single-end sequencing data
    • Format: Parameter value (pair/unpaired)

Optional Inputs

  • Denatured Sample Directory

    • Description: Directory containing sequencing data from denatured RNA samples for background correction
    • Format: Directory containing FASTQ files

  • Sample Name

    • Description: Custom name for the analysis run
    • Format: Text string

Outputs

  • Results Directory

    • Description: Complete analysis results including all processed files and reports
    • Format: Directory

  • Mutation Files

    • Description: Parsed and processed mutation data files
    • Format: Mutation files (.mut)

  • Text Report

    • Description: Summary statistics and analysis results in text format
    • Format: Text file (.txt)

  • Flowchart Visualization

    • Description: Visual representation of the analysis pipeline and data flow
    • Format: SVG file (.svg)

  • Analysis Report

    • Description: Comprehensive analysis report with visualizations
    • Format: PDF file (.pdf)

Parameters & Settings

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

  • DMS

    • Description: Run using DMS mode. Data will be normalized on a per-nucleotide basis. Note that this option is optimized for DMS-MaP data collected using Marathon and/or TGIRT enzymes.
    • Available options: true, false (default)

  • max-bg

    • Description: Maximum allowed mutation frequency in untreated sample.
    • Default value: 0.05

  • Choose aligner

    • Description: Use Bowtie2 or STAR for sequence alignment. STAR is recommended for sequences longer than several thousand nucleotides. STAR may also be slightly less sensitive than Bowtie2 (fewer aligned reads).
    • Available options: Bowtie2 (default), STAR

  • Amplicon

    • Description: Require reads to align near expected primer pair locations, and intelligently trim primer sites.
    • Available options: false (default), true

  • Minimum Depth

    • Description: Minimum effective sequencing depth for including data (threshold must be met for all provided samples).
    • Default value: 5000

  • Normalize individually

    • Description: Normalize multiple reactivity profiles individually, instead of as a group.
    • Available options: false (default), true

  • Render Flowchart

    • Description: Render a flowchart (SVG format) in the output folder depicting all data processing components and input/output files.
    • Available options: true (default), false

  • Parsed Mutations

    • Description: Produce output files for selected intermediate components (parsed mutations).
    • Available options: true (default), false

References & Resources

  • Tool Documentation: Contact the team for details on ShapeMapper2 analysis pipeline
  • Related Papers: Busan, S. & Weeks, K.M. Accurate detection of chemical modifications in RNA by mutational profiling (MaP) with ShapeMapper 2. RNA 24, 143-174 (2018). DOI: 10.1261/rna.061945.117