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deepTools CreateMatrix Specifications

Process Details

  • Name: deepTools CreateMatrix
  • Process UUID: 4944fb0472404cda828502f9d23effc7
  • Process Group: Misc.

Overview

This process creates a matrix from bigWig and BED files using deepTools' computeMatrix function in scale-regions mode. The process is designed to generate data matrices that can be used for downstream visualization and analysis of genomic signal data, particularly useful for creating heatmaps and profile plots around genomic features such as genes or regulatory elements.

This process is implemented in Bash, which invokes deepTools for matrix computation and genomic signal analysis.

Key Functionality

  • Matrix Generation: Creates a numerical matrix from bigWig signal files and genomic regions defined in BED format
  • Region Scaling: Uses scale-regions mode to normalize regions to a consistent length while preserving relative signal patterns
  • Signal Processing: Handles missing data and zero values appropriately for downstream visualization
  • Customizable Parameters: Allows adjustment of bin size, region lengths, and labeling for flexible analysis

Input/Output Specification

Inputs

Required Inputs

  • bigWig Tuple

    • Description: Set of bigWig files containing genomic signal data (e.g., ChIP-seq, ATAC-seq, RNA-seq coverage)
    • Format: bigWig (.bw)

  • BED File

    • Description: Genomic regions file defining the features around which to compute the matrix
    • Format: BED (.bed)

Outputs

  • Zipped Matrix File
    • Description: Compressed matrix file containing computed signal values that can be used for heatmap generation and profile plotting
    • Format: Gzipped (.gz)

Parameters & Settings

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

  • Start Label

    • Description: Label shown in the plot for the start of the region. Default is TSS (transcription start site), but could be changed to anything, e.g. 'peak start'. Note that this is only useful if you plan to plot the results yourself and not, for example, with plotHeatmap, which will override this.
    • Default value: TSS

  • End Label

    • Description: Label shown in the plot for the region end. Default is TES (transcription end site). See the Start Label option for more information.
    • Default value: TES

  • Bin Size

    • Description: Size of bins in base pairs for matrix computation
    • Default value: 50

  • Before Region Start Length

    • Description: Length in base pairs to extend before the start of each region
    • Default value: 1000

  • Region Body Length

    • Description: Length in base pairs to scale the region body to
    • Default value: 3000

  • After Region Start Length

    • Description: Length in base pairs to extend after the end of each region
    • Default value: 1000

References & Resources

  • Tool Documentation: deepTools documentation
  • Related Papers: Ramírez, F., Ryan, D. P., Grüning, B., Bhardwaj, V., Kilpert, F., Richter, A. S., ... & Manke, T. (2016). deepTools2: a next generation web server for deep-sequencing data analysis. Nucleic acids research, 44(W1), W160-W165.