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RNAFramework Norm Specifications

Process Details

  • Name: RNAFramework_Norm
  • Process UUID: 90d672597de64b1a8e2c0f523d698d91
  • Process Group: Misc.

Overview

RNAFramework Norm performs normalization of RNA structure probing data using the RNA Framework toolkit. This process takes mutation count data from RNA structure probing experiments and applies various scoring and normalization methods to generate transcript reactivity profiles. The process is designed to handle different experimental protocols including SHAPE, DMS, and other chemical probing methods.

This process is implemented in Bash, which invokes the RNA Framework's rf-norm tool for data normalization and analysis.

Key Functionality

  • Multi-method Scoring: Supports four different scoring methods including Ding et al. (2014), Rouskin et al. (2014), Siegfried et al. (2014), and Zubradt et al. (2016) approaches
  • Flexible Normalization: Offers four normalization methods including 2-8%, 90% Winsorizing, Box-plot, and Mitchell et al. (2023) methods
  • Experiment-specific Processing: Handles different chemical probing experiments (SHAPE, DMS, custom) with appropriate reactive base considerations
  • Comparative Analysis: Processes paired untreated/treated samples with optional denatured controls
  • Visualization Output: Generates normalization plots and quality control images

Input/Output Specification

Inputs

Required Inputs

  • mutation

    • Description: RNA mutation count data from structure probing experiments
    • Format: rc (read count format)

  • rc_index

    • Description: Index file corresponding to the mutation count data
    • Format: index

Outputs

  • transcript_reactivity

    • Description: Normalized transcript reactivity profiles containing per-nucleotide reactivity scores
    • Format: xml

  • directory

    • Description: Output directory containing organized results, normalization plots, and processed data files
    • Format: directory

Parameters & Settings

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

  • Scoring Method

    • Description: [1] Ding et al., 2014
      [2] Rouskin et al., 2014
      [3] Siegfried et al., 2014
      [4] Zubradt et al., 2016
    • Available options: 1 (default), 2, 3, 4

  • Normalization Method

    • Description: [1] 2-8%
      [2] 90% Winsorizing
      [3] Box-plot
      [4] Mitchell et al., 2023
      Note: 2-8% and Box-plot normalization methods cannot be used with Rouskin scoring method
    • Available options: 1 (default), 2, 3, 4

  • Experiment type

    • Description: Determines the reactive bases in the study.
      SHAPE: ACGT
      DMS: AC
      Other: You can determine the reactive bases yourself
    • Available options: SHAPE (default), DMS, Other

  • Reactive Bases

    • Description: Reactive bases to consider for signal normalization
    • Default value: all

  • Normalize independently

    • Description: Each reactive base will be normalized independently
    • Default value: false

  • Other Normalization Parameters

    • Description: Additional parameters for the normalization process
    • Default value: (empty)

References & Resources

  • Tool Documentation: Contact the team for details on rf-norm
  • Related Papers: Incarnato, D. et al. (2018). RNA Framework: an all-in-one toolkit for the analysis of RNA structures and post-transcriptional modifications. Nucleic Acids Research, 46(16), e97. https://doi.org/10.1093/nar/gky486