Spiker’s Documentation

Introduction

• Introduction to spike-in control

Installation

• 1. Prerequisites
• 2. Python Dependencies
• 3. Install Spiker
• 4. Upgrade Spiker
• 5. Uninstall

Usage information

• 1. Analysis workflow
• 2. Input and output
• 3. Spiker.py options
• 4. split_bam.py options

Walkthrough example

• 1. Prepare FASTQ files
• 2. Build bowtie2 index files
• 3. Map reads to the composite reference genome
• 4. Calculate scaling factors
• 5. Run Spiker

Bowtie2 Index Files

• 1. Bowtie2 index files
• 2. Index files for Human + Drosophila
• 3. Index files for Mouse + Drosophila

Test Dataset

• 1. Test dataset
• 2. H3K79me2 ChIP-seq data
• 3. WCE (whole cell extract) data
• 4. MD5sum

Release history

• 1. Release history
  • 1.1. Version 1.0.0

Liscense

• LICENSE

Reference

• Reference