Welcome to the documentation of diffTF!

Welcome to the diffTF documentation, and thank you for the interest in our software! These pages provide documentation and additional information for the diffTF pipeline.

To get yourself oriented, check the menu on the left or search what you are looking for in the search field in the upper left corner.

This site is organized into the following three parts:

Quick Start and Installation

• Try it out now!
• Prerequisites for the “easy” way
• Prerequisites for the “manual” way
  • Snakemake
  • samtools, bedtools, Subread
  • R and R packages
• Run your own analysis
• Adaptations and notes when running with Singularity

Pipeline Details

• Workflow
• Input
  • Summary
  • General configuration file
  • Input metadata
• Output
  • FOLDER FINAL_OUTPUT
  • FOLDER PEAKS
  • FOLDER TF-SPECIFIC
  • FOLDER LOGS_AND_BENCHMARKS
  • FOLDER TEMP
• Running diffTF
  • General remarks
  • Executing diffTF - Running times and memory requirements
  • Running diffTF in a cluster environment
• Frequently asked questions (FAQs)
• Handling errors
  • Error types
  • Identify the cause
  • Common errors
  • Fixing the error
• Understanding and interpreting results
  • General notes
  • Specifics for the basic mode
  • Specifics for the classification mode

Project Information

• Biological motivation
• Example dataset
• Help, contribute and contact
• Citation
• Change log
• License