Welcome to chromTools’ documentation

chromTools complete is a tool for assessing the completeness of an epigenetic dataset. The tool aims to provide the user with the ability to assesses the extent to which their epigenetic dataset captures the complete set of marks, using a subsampling approach to estimate the number of reads required to approach the complete sampling of the mark. It uses BED files as input for ChIP-seq and WGBS data and shifted tagAlign files (BED) as input for ATAC-seq data.

Note

This project is under active development.

Contents

• Overview
  • Why chromTools?
  • What does chromTools do?
    • chromTools complete
• Installation
• General Usage
  • Input
    • Required columns
    • Example pipeline and input file
  • Output
  • Basic usage
    • Required parameters
    • Optional parameters
  • Example Usage
  • Interpretation
• Internal Functions
  • chromTools complete

Indices

• Index