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RNAFramework Combine Specifications

Process Details

  • Name: RNAFramework Combine
  • Process UUID: 0053c55814b040adaf2afcede2938543
  • Process Group: Misc.

Overview

RNAFramework Combine is a specialized process that merges multiple RNA structure probing experiments into a single comprehensive XML profile. This process is essential for combining replicate experiments or integrating data from different experimental conditions to create unified reactivity profiles for downstream RNA structure analysis.

This process is implemented in Bash, which invokes the rf-combine tool from the RNAFramework suite for XML profile integration.

Key Functionality

  • Multi-experiment Integration: Combines multiple XML reactivity profiles from different experiments into a single unified profile
  • Statistical Correlation Analysis: Calculates correlation between replicates using Pearson or Spearman correlation algorithms to assess data quality
  • Replicate Averaging: Computes mean reactivities across replicates with optional standard deviation reporting for error estimation
  • Data Transformation: Provides optional log transformation of reactivity values before averaging to handle non-normal distributions

Input/Output Specification

Inputs

Required Inputs

  • Transcript Reactivity
    • Description: XML files containing RNA reactivity profiles from individual experiments or replicates
    • Format: XML

Outputs

  • Transcript Reactivity
    • Description: Combined XML profile containing merged reactivity data from all input experiments with correlation statistics
    • Format: XML

Parameters & Settings

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

  • Correlation Algorithm

    • Description: Uses Spearman instead of Pearson to calculate correlation. Pearson: Assumes the correlation calculations are done for normally distributed, parametric data. Spearman: Correlation calculation for non-parametric data
    • Available options: Pearson (default), Spearman

  • Do Log Transformation?

    • Description: Log transforms values before averaging replicates
    • Default value: false

  • Other Parameters

    • Description: -s or --stdev: When combining multiple replicates, an optional "-error" tag will be reported in the output XML files, containing the per-base standard deviation of the measure. -d or --decimals [int]: Number of decimals for reporting reactivities (1-10, Default: 3). -m or --min-values [float]: Minimum number of values to calculate correlation (Default: off). Note: if a value between 0 and 1 is provided, this is interpreted as a fraction of the transcript's length. -c or --min-correlation [float]: Minimum correlation to report a combined profile (-1-1, Default: off). Note: if more than two replicates are being combined, RF Combine requires this threshold to be satisfied by all pairwise comparisons. -i or --ignore-NaNs: NaNs are ignored when calculating mean reactivities. Note: this parameter enables combining XML files from experiments with different sets of reactive bases (e.g., A/C and G/U)
    • Default value: (empty)

References & Resources

  • Tool Documentation: Contact the team for details on rf-combine