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ATAC CHIP Summary Specifications

Process Details

  • Name: ATAC CHIP summary
  • Process UUID: 20bdd6c8-ed05-11e8-9ce4-85221b21564c
  • Process Group: Misc.

Overview

This process summarizes ATAC-Seq or ChIP-Seq alignment results by consolidating data from multiple sample files into a unified tabular format. It processes individual summary files containing alignment statistics and feature counts, then generates a comprehensive matrix showing counts across all samples for comparative analysis.

This process is implemented in Perl.

Key Functionality

  • File Discovery and Processing: Automatically identifies and processes all .txt summary files in the working directory
  • Data Consolidation: Extracts feature counts from individual sample files and consolidates them into a single matrix
  • Sample Organization: Organizes data by sample names (derived from filenames) and genomic features
  • Matrix Generation: Creates a tab-separated values file with features as rows and samples as columns

Input/Output Specification

Inputs

Required Inputs

  • outputFileTxt
    • Description: Text files containing ATAC-Seq or ChIP-Seq alignment summary statistics and feature counts for individual samples
    • Format: txt

Outputs

  • outputFile
    • Description: Consolidated summary table containing feature counts across all input samples in matrix format
    • Format: tsv

Parameters & Settings

This process does not have user-configurable parameters in the Foundry UI.

References & Resources

  • Tool Documentation: Contact the team for details on the custom Perl summarization script