CAMPAREE Documentation

User Guide

• Introduction
  • ABOUT
• Quick Start Guide
  • Installation
  • Baby Genome
    • Perform Test Run
    • Check Results
• Installing CAMPAREE
  • General Instructions
  • Installing CAMPAREE on AWS
    • Single Instance in Serial Mode
    • AWS ParallelCluster in SGE Mode
• Running CAMPAREE
  • Command Line Options
• Resource Files
  • Overview
  • File Descriptions
    • Reference Genome Sequence File
    • Transcript Annotation File
    • Chromosome Ploidy File
    • STAR Genome Index
  • Pre-Built Resource Files
    • Download Links for Pre-Built Resource Files
  • Generating Custom Resource Files
• CAMPAREE Output
  • Using CAMPAREE with other RNA-seq simulators
    • Preparing CAMPAREE Output
    • Polyester
    • BEERS
    • RSEM

The API Reference

• CAMPAREE API
  • The CAMPAREE Controller
  • Expression Simulation Pipeline
  • Genome Alignment & BAM Indexing Steps
  • Variant Finder Step
  • Intron Quantification Step
  • Variant Compilation Step
  • Beagle Step
  • Genome Builder Step
  • Update Annotation Step
  • Transcriptome FASTA Preparation Step
  • Kallisto Index Generation & Quantification Steps
  • Bowtie2 Index Generation & Alignment Steps
  • Transcript Quantification Step
  • Allelic Imbalance Quantification Step
  • Molecule Maker Step
  • Annotation Info
  • CAMPAREE Utils
  • Abstract CAMPAREE Step
  • CAMPAREE Step Provider
  • CAMPAREE Constants

Indices and tables

• Index

• Module Index

• Search Page