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TE Summary Specifications

Process Details

  • Name: TE Summary
  • Process UUID: nr9dw9ednx3xwtig7kgkuu5i8oj8fg
  • Process Group: TE Transcripts

Overview

The TE Summary process aggregates transposable element (TE) transcript counts from multiple input files into a single consolidated TSV file. This process is essential for downstream analysis of TE expression patterns across samples, enabling researchers to study the activity and regulation of repetitive genetic elements in their datasets.

This process is implemented in Bash, which invokes a Python script for TE count aggregation.

Key Functionality

  • Count Aggregation: Combines TE transcript count data from multiple TSV files into a unified dataset
  • Data Consolidation: Merges sample-specific TE quantification results for comparative analysis
  • Output Standardization: Produces a standardized TSV format suitable for downstream statistical analysis

Input/Output Specification

Inputs

Required Inputs

  • Input File TSV
    • Description: TSV files containing transposable element transcript count data from individual samples
    • Format: TSV (Tab-separated values)

Outputs

  • Output File TSV
    • Description: Consolidated TSV file containing aggregated TE transcript counts across all input samples
    • Format: TSV (Tab-separated values)

References & Resources

  • Tool Documentation: Contact the team for details on collect_TE_counts.py