CluBCpG: Cluster-Based analysis of CpG methylation

What is CluBCpG?

CluBCpG is a software package built to analyze whole genome bisulfite sequencing (WGBS) data. This toolkit will divide each chromosome into small user-defined intervals, extract all WGBS reads within those intervals, cluster them based on identity, and write a final report to the use containing all identified CpG methylation patterns.

CluBCpG supports both paired-end and single-end data and any read-length. However, a read length of at least 100 base-pairs is recommended

CluBCpG is written 100% in Python, but CluBCpG requires no knowledge of python (or any programming language) to use.

CluBCpG was created to be primarily utilized as command line based tools, but it does provide a few APIs which may be useful on their own for researchers. Those APIs are documented in API documentation.

User Guide Contents:

• 1. Getting Started
  • 1.1. Requirements
  • 1.2. Installation
    • 1.2.1. pip install
  • 1.3. Running Tests
• 2. Using CluBCpG
  • 2.1. Introduction
  • 2.2. Sequencing data pre-processing
  • 2.3. Typical workflow
    • 2.3.1. Prepare your data
    • 2.3.2. Calculate bin coverage
    • 2.3.3. Filter output
    • 2.3.4. Perform clustering
  • 2.4. Command line tools
    • 2.4.1. clubcpg-coverage
    • 2.4.2. clubcpg-cluster
• 3. Understanding the CluBCpG output data
  • 3.1. Coverage output
  • 3.2. Cluster output
• 4. Using CluBCpG with PReLIM
  • 4.1. Introduction
  • 4.2. Typical imputation workflow
    • 4.2.1. Calculate bin coverage
    • 4.2.2. Filter outputs
    • 4.2.3. Train a PReLIM model
    • 4.2.4. Compute coverage gains
    • 4.2.5. Filter imputed coverage output
    • 4.2.6. Perform clustering with imputation
  • 4.3. Command line tools
    • 4.3.1. clubcpg-impute-train
    • 4.3.2. clugcpg-impute-coverage
    • 4.3.3. clubcpg-impute-cluster

Developer Reference:

• API documentation
  • ClubCpG APIs
  • PReLIM APIs

Indices and tables

• Index

• Module Index

• Search Page