Welcome to ALISEQ’s documentation!

Contents:

• ALISEQ, a program for analysing RNA-Seq data
• Instalation and setup
  • Download the source code
  • Test if it’s working
• Running the allele specific expression (ASE) pipeline
  • Edit the file targets.txt
  • Modifying workflow parameters
  • Running the workflow
• Running the read simulation pipeline
  • Modifying simulation parameters
  • Running the workflow
• Workflow
• Other stuff
• Python modules
  • simulate_reads.py
  • genewiseMAFC.py
  • maketable.py
  • convert2bed.py
  • read_buffalo_xml_data.py
  • evaluate_simulation.py

Indices and tables

• Index
• Module Index
• Search Page